Attenuated live bacteria with increased acid resistance and methods of use thereof

ABSTRACT

The present invention relates to inducing acid resistance in a bacterium and methods of increasing the acid resistance of an acid sensitive bacterium.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the priority of U.S. provisional application No.61/836,140, filed Jun. 17, 2013, which is hereby incorporated byreference in its entirety.

GOVERNMENTAL RIGHTS

This invention was made with government support under 1R21A1092307awarded by the National Institutes of Health. The government has certainrights in the invention.

FIELD OF THE INVENTION

The present invention relates to inducing acid resistance in a bacteriumand methods of increasing the acid resistance of an acid sensitivebacterium.

BACKGROUND OF THE INVENTION

In order to reach their intestinal habitat, enteric microbes must firstsurvive the formidable low pH environment of the stomach, making anacid-coping strategy imperative. Wild-type Salmonella enterica serotypeshave multiple ways to resist low pH. First, the acid tolerance response(ATR) upregulates acid shock proteins to temporarily prevent cellulardamage. Second, the acid resistance systems (AR) consume protons toraise the intracellular pH. AR1 system is regulated by Crp and is poorlyunderstood. The remaining systems, AR3, AR4 and AR5 (AR2 is not presentin Salmonella) rely on arginine, lysine and ornithine decarboxylases,respectively. However, AR3-5 are typically repressed under standardlaboratory growth conditions, and the ATR in many live attenuatedSalmonella vaccines is impaired, making gastric transit challenging forthese strains. In addition, many means used to attenuate Salmonella forvirulence have a secondary effect of increasing sensitivity to acid,thereby increasing the effective dose required for immunogenicity. As aresult, oral Salmonella vaccines are typically given with an agentdesigned to increase the gastric pH, such as bicarbonate. While thisapproach is helpful, it precludes the Salmonella vaccine from sensingimportant environmental signals (i.e. low pH) that optimize its abilityto effectively interact with host tissues. This results in reducedimmunogenicity as a vaccine.

SUMMARY OF THE INVENTION

In an aspect, the invention encompasses a recombinant attenuatedderivative of a pathogenic enteric bacterium comprising at least one ofthe following: a regulatable promoter operably linked to a nucleic acidencoding an arginine decarboxylase and a nucleic acid encoding anarginine agmatine antiporter; a regulatable promoter operably linked toa nucleic acid encoding a glutamate decarboxylase and a nucleic acidencoding a glutamate/γ-aminobutyric acid antiporter; or a regulatablepromoter operably linked to a nucleic acid encoding a lysinedecarboxylase and a nucleic acid encoding a lysine/cadaverineantiporter.

In another aspect, the invention encompasses a method for increasing theacid resistance of an acid sensitive bacterium, the method comprisingintroducing into the acid sensitive bacterium a cassette comprising atleast one of the following: a regulatable promoter operably linked to anucleic acid encoding an arginine decarboxylase and a nucleic acidencoding an arginine agmatine antiporter; a regulatable promoteroperably linked to a nucleic acid encoding a glutamate decarboxylase anda nucleic acid encoding a glutamate/γ-aminobutyric acid antiporter; or aregulatable promoter operably linked to a nucleic acid encoding a lysinedecarboxylase and a nucleic acid encoding a lysine/cadaverineantiporter, such that in the absence of induction of the regulatablepromoter, the recombinant bacterium is acid sensitive, but uponinduction of the regulatable promoter, the recombinant bacteriumdisplays an increase in acid resistance.

A recombinant Salmonella bacterium, the bacterium comprising aregulatable promoter operably linked to at least one nucleic acidselected from the group consisting of adiA and adiC; gadB and gadC; andcadB and cadA.

BRIEF DESCRIPTION OF THE FIGURES

The application file contains at least one drawing executed in color.Copies of this patent application publication with color drawing(s) willbe provided by the Office upon request and payment of the necessary fee.

The following drawings form part of the present specification and areincluded to further demonstrate certain aspects of the presentinvention. The invention may be better understood by reference to one ormore of these drawings in combination with the detailed description ofspecific embodiments presented herein.

FIG. 1. Schematic diagram of arginine decarboxylase mutations. The genesand associated regulatory sequences for the Δ(adiA-adiC), ΔP_(adiA)::TTaraC P_(araBAD) adiA, ΔP_(adiA):TT rhaSR P_(rhaBAD) adiA, andΔ(P_(adiY)-adiY-P_(adiC)) adiC mutations are shown above, along with thearchetypal strain number. The wild-type arginine decarboxylase locus(adi) of S. Typhi Ty2 is depicted for comparative purposes. The diagramis approximately to scale. (

) promoter; (

) transcription terminator.

FIG. 2. Regulation of adiA by the araC P_(araBAD) and rhaSR P_(rhaBAD)promoters. χ11552 (ΔaroD P_(araBAD) adiA) and χ11564 (ΔaroD P_(rhaBAD)adiA) were cultured in the presence of varying concentrations ofarabinose or rhamnose (ranging from 10⁻¹-10⁻⁵%), normalized and (A)assayed by semi-quantitative PCR for the level of adiA transcript, (B)probed for the presence of AdiA by western blot or (C) tested forarginine decarboxylase activity via colorimetric assay. mRNA data areplotted as the mean and SEM of three independent experiments. Westernblot and enzyme assay data are representative of three independentassays. In the colorimetric arginine decarboxylase assay, a dark bluecolor is indicative of the presence of AdiA.

FIG. 3. Co-regulation of adiA and adiC by rhamnose is required forsurvival during pH 3 challenge. χ11564 (ΔaroD P_(rhaBAD) adiA), χ11568(ΔaroD P_(rhaBAD) adiAC) and χ11636 (ΔaroD adiAC) were grown tostationary phase in EG medium in the presence of 0.1% rhamnose, thenchallenged with pH 3.0 EG medium containing 1 mM arginine. Survival wasmonitored by plating on LB agar containing all necessary supplements.Data shown are the mean and SEM of three independent assays.

FIG. 4. Acid resistance depends on the presence of rhamnose andarginine. Ty2, χ11548 (ΔaroD) and χ11568 (ΔaroD P _(rhaBAD) adiAC) weregrown to stationary phase in EG medium, then challenged with EG medium,pH 3.0. (A) Strains cultured in the presence or absence of 0.1%rhamnose. (B) Strains challenged in the presence or absence of 1 mMarginine. Survival in all assays was monitored by plating on LB agarcontaining all necessary supplements. Data shown are the mean and SEM ofthree independent assays.

FIG. 5. Acid resistance of an ΔaroD mutant containing rhamnose-regulatedarginine decarboxylase at pH 2.5. Ty2, χ11500 (ΔadiA-adiC), χ11548(ΔaroD) and χ11568 (ΔaroD P_(rhaBAD) adiAC) were grown to stationaryphase in EG medium containing 0.1% rhamnose, then challenged with EGmedium containing 1 mM arginine at pH 2.5 for 1 hour. Survival in allassays was monitored by plating on LB agar containing all necessarysupplements. Data shown are the mean and SEM of three independentassays. Pairs of data marked with an asterisk (*) are significantlydifferent (p<0.05).

FIG. 6. Acid resistance of a ΔphoPQ mutant containing rhamnose-regulatedarginine decarboxylase. Ty2, χ11500 (ΔadiA-adiC), χ8444 (ΔphoPQ) andχ11622 (ΔphoPQ P_(rhaBAD) adiAC) were grown to stationary phase in EGmedium containing 0.1% rhamnose, then challenged with EG mediumcontaining 1 mM arginine at (A) pH 3.0 for 4 hours or (B) pH 2.5 for 1hour. Survival in all assays was monitored by plating on LB agarcontaining all necessary supplements. Data shown are the mean and SEM ofthree independent assays. Pairs of data marked with an asterisk (*) aresignificantly different (p<0.05).

FIG. 7. Acid resistance of a ΔP_(fur)::TT araC P_(araBAD) fur mutantcontaining rhamnose-regulated arginine decarboxylase. (A) Strains weregrown overnight in purple broth ±0.2% arabinose, then probed for thepresence of Fur by western blot. (B) χ11118 was grown to stationaryphase in EG medium ±0.2% arabinose, then challenged with EG mediumcontaining 1 mM arginine at pH 3.0 for 4 hours. Arginine decarboxylaserescue was performed by growing strains in EG medium to stationary phasein the absence of arabinose and presence of 0.1% rhamnose andchallenging with EG medium containing 1 mM arginine at (C) pH 3.0 for 4hours or (D) pH 2.5 for 1 hour. Survival in all assays was monitored byplating on LB agar containing all necessary supplements. Data shown arethe mean and SEM of three independent assays. Pairs of data marked withan asterisk (*) are significantly different (p<0.05). χ11500=ΔadiA-adiC;χ11118=P_(araBAD) fur; χ11623=P_(araBAD) fur P_(rhaBAD) adiAC;χ11742=Δfur

FIG. 8. Comparison of acid resistance provided by native andrhamnose-regulated arginine decarboxylase. Strains containing (A, B)ΔaroD (C, D) ΔphoPQ or (E, F) ΔP_(fur)::TT araC P_(araBAD) furattenuating mutations were grown overnight in TSB medium with 0.4%glucose and 0.1% rhamnose under anaerobic conditions. For χ11623, 0.4%rhamnose was supplied. Cells were challenged with EG medium containing 1mM arginine, pH 3.0 (A, C, E) or pH 2.5 (B, D, F). Survival in allassays was monitored by plating on LB agar containing all necessarysupplements. Data shown are the mean and SEM of three independentassays. 11500=ΔadiA-adiC; 11548=ΔaroD; 11568=ΔaroD P_(rhaBAD) adiAC;8444=ΔphoPQ; 11622=ΔphoPQ P rhaBAD adiAC; 11118=P_(araBAD) fur;11623=P_(araBAD) fur P_(rhaBAD) adiAC.

FIG. 9. Schematic diagram of glutamate decarboxylase constructions. Thegenes and associated regulatory sequences for the ΔcysG and ΔcysG::TTaraC P_(BAD) gadBC mutations are shown above along with the hypotheticalsequence mutations ΔaraE and ΔaraE::TT araC P_(BAD) gadA. The wild-typecysG and araE loci of S. Typhi Ty2 are depicted for comparativepurposes. The diagram is approximately to scale. (

) promoter; (

) transcription terminator.

FIG. 10. Survival of S. Typhi strains during in vitro low pH challenge.Strains were grown to stationary phase in EGA medium, pH 7.0 containingarabinose with aeration, then washed and challenged in EG mediumcontaining 1 mM glutamic acid. ΔguaBA, ΔphoPQ, and Δfur mutants werechallenged at pH 3.0 (A) or pH 2.5 (B) for 1 h. Data are presented asthe mean and SEM for each time point.

FIG. 11. Gastric pH following histamine injection. Following a 6 hourfast, mice were injected subcutaneously with 10 mg/kg histamine. Micewere anaesthetized with pentobarbital prior to gastric surgery. GastricpH was measured at the mucosal surface of the stomach for up to 4 hourspost histamine injection. Data shown are the mean and standard deviationof at least five mice per time point.

FIG. 12. Survival of strains cultured under non-acid resistance inducingconditions. Wild-type enteric strains were grown in LB medium to latelog phase under aerobic conditions. (A) Cells were washed and challengedin EG medium (pH 3.0) containing 0.1% casamino acids. Survival during EGmedium challenge was assayed hourly for 4 hours by plating onto LB agar.Data shown are the mean and SEM of three independent experiments. (B)Cells were washed and then resuspended in PBS containing 0.1% casaminoacids. Mice were either fasted for 6 hours (fasted mouse model) orfasted and low gastric pH was induced by histamine injection (acid mousemodel) and then inoculated with 10⁹ CFU of each strain. Cells containedthe pWSK129 plasmid (Kan^(R)) to enhance recovery from intestinaltissues. Sixty minutes after inoculation, mice were euthanized and theentire small intestine removed and homogenized. Survival was assayed byplating onto LB agar containing kanamycin. Data are expressed as thepercent of initial inoculum recovered (% survival). The geometric meanand 95% confidence interval of two independent experiments (8 micetotal) is depicted.

FIG. 13. Effect of arginine decarboxylase on the gastric survival of S.Typhi. Pairs of attenuated S. Typhi strains differing only in theirarginine decarboxylase locus were grown to stationary phase in EGAmedium under aerobic conditions. Cells were combined in a 1:1 ratio inPBS containing 1 mM arginine. Low gastric pH was induced by histamineinjection in mice fasted for 6 h. Mice were inoculated with 10⁹ CFU ofeach strain. Sixty min after inoculation, mice were euthanized and theentire small intestine removed and homogenized. Strain survival wasassayed by plating onto LB agar containing kanamycin or streptomycin.Data shown are the competitive index of the two strains in each mousewith the geometric mean of two independent experiments (10 mice total)indicated as a solid line.

FIG. 14. Effect of glutamate decarboxylase on the gastric survival of S.Typhi. Pairs of attenuated S. Typhi strains differing only in theirglutamate decarboxylase locus were grown to stationary phase in EGAmedium under aerobic conditions. Cells were combined in a 1:1 ratio inPBS containing 1 mM glutamic acid. Low gastric pH was induced byhistamine injection in mice fasted for 6 h. Mice were inoculated with10⁹ CFU of each strain. Sixty min after inoculation, mice wereeuthanized and the entire small intestine removed and homogenized.Strain survival was assayed by plating onto LB agar containing kanamycinor streptomycin. Data shown are the competitive index of the two strainsin each mouse with the geometric mean of two independent experiments (10mice total) indicated as a solid line.

FIG. 15. Survival of S. Gallinarum strains during low pH challenge.Mid-log aerobic cultures grown in LB broth were harvested, washed andchallenged with E medium at pH 3.0. Samples were taken and numbers ofsurviving cells were determined by direct plating onto LB plates. Dataare presented as the mean and SEM for each time point.

FIG. 16. Rescue of acid sensitive S. Gallinarum strains byarabinose-inducible gadBC system. Cultures were grown aerobically in LBbroth to an optical density at 600 nm of 0.4. Cells were harvested,washed and challenged with E medium at pH 3.0 for one hour. Numbers ofsurviving cells were determined by direct plating onto LB plates. Dataare presented as the mean and SEM for each time point.

FIG. 17. Survival of RASV strains during low pH gastric transit.Histamine-treated mice were inoculated orally with 10⁹ CFU of (A)χ9633(pYA4088, pWSK129), (B) χ9639(pYA4088, pWSK129), (C) χ9640(pYA4088,pWSK129) or (D) χ9558(pYA4088, pWSK129). Mice received either 1.3%sodium bicarbonate, chocolate Ensure or nothing prior to and immediatelyfollowing immunization to neutralize gastric acid. The number of viablevaccine cells in the small intestine was quantified one hour afterimmunization. Data are presented as the number of CFU/g intestine ofindividual mice, with the geometric mean of the group displayed as asolid horizontal line. Groups that exhibited a significant increase(p<0.05) in the number of viable vaccine cells in the small intestineover the control group are marked with an asterisk (*). Data are thecombined results of two independent experiments (8 mice total).

DETAILED DESCRIPTION

The present invention encompasses a bacterium with increased acidresistance, methods of increasing the acid resistance of a bacterium,and methods of use thereof. The invention also encompasses vaccinecompositions comprised of a bacterium exhibiting an increase in acidresistance. Advantageously, a bacterium with an increase in acidresistance of the invention may be administered orally to a subject andsubstantially survive the low pH of the subject's stomach, whileexposure to the low pH environment stimulates up-regulation of invasionand/or virulence related nucleic acid sequences.

I. Recombinant Attenuated Bacterium

A recombinant bacterium of the invention is typically a bacterialenteric pathogen, and belongs to a species or strain commonly used for avaccine.

Enteric pathogenic bacteria are agents of intestinal disease typicallyacquired through ingestion. These pathogens include, but are not limitedto, bacteria of the family Enterobacteriaceae, such as Salmonellaspecies, Shigella species, Yersinia species (e.g. Y. pseudotuberculosisand Y. enterocolitica), certain pathovars of Escherichia coli, includingenterotoxigenic E. coli (ETEC), enterohaemorrhagic E. coli (EHEC),enteropathogenic E. coli (EPEC) and extraintestinal E. coli (ExPEC).Other enteric pathogens include Vibrio species (e.g. V. cholerae) andthe gram-positive bacterium Listeria monocytogenes.

To be safe for use as a vaccine, the bacterial enteric pathogen must beattenuated for virulence by deletion or regulated expression of avirulence gene. In the case of Salmonella, for instance, the followinggenes may be altered to achieve attenuation: pab, aroA, aroC, aroD,asdA, dapA, dam, murA, nadA, pncB, galE, pmi, fur, ompR, htrA, hemA,cdt, cya, crp, phoP, phoQ, rfc, rfaH, poxA, galU, guaB, guaA, hfq, msbBor genes required for the function of type 3 secretion systems inpathogenicity island 2, such as ssaV, or an effector molecule secretedby the type 3 secretion system, such as sopB. The genes may be deletedor a regulatable promoter may be inserted in front of the gene toachieve regulated delayed attenuation. As used herein, “regulateddelayed attenuation” refers to the ability of the microbe to colonize ahost and then display an attenuation phenotype to avoid actually causinga symptomatic infection.

In the case of Shigella, these genes may include guaA, guaB, senA, senB,set, aroA, virG, msbB, icsA, iuc, iutA, ipaB, ipaC, ipaD, ipaA. Thegenes may be deleted or a regulatable promoter may be inserted in frontof the gene to achieve regulated delayed attenuation.

In the case of E. coli, attenuating mutations may include deletions inompF, ompC, ompR, aroA, aroC, aroD, astA, eltB, eltA, estA, cya, crp.The genes may be deleted or a regulatable promoter may be inserted infront of the gene to achieve regulated delayed attenuation.

In some embodiments, a recombinant bacterium of the invention is aspecies or subspecies of the Salmonella genera. For instance, therecombinant bacterium may be a Salmonella enterica serovar. In anexemplary embodiment, a bacterium of the invention may be derived fromS. Typhimurium, S. Typhi, S. Paratyphi, S. Gallinarum, S. Enteritidis,S. Choleraesius, S. Arizona, or S. Dublin. In another exemplaryembodiment, a bacterium of the invention may be an S. Typhi bacterium.In yet another exemplary embodiment, a bacterium of the invention may bean S. Typhi Ty2 bacterium. In yet still another exemplary embodiment, abacterium of the invention may be an S. Gallinarum bacterium. In stillyet another exemplary embodiment, a bacterium of the invention may be anS. Dublin bacterium.

A recombinant bacterium of the invention derived from Salmonella may beparticularly suited for use as a vaccine. Infection of a host with aSalmonella strain typically leads to colonization of the gut-associatedlymphoid tissue (GALT) or Peyer's patches, which leads to the inductionof a generalized mucosal immune response to the recombinant bacterium.Further penetration of the bacterium into the mesenteric lymph nodes,liver and spleen may augment the induction of systemic and cellularimmune responses directed against the bacterium. Thus the use ofrecombinant Salmonella for oral immunization stimulates all threebranches of the immune system, which is particularly important forimmunizing against infectious disease agents that colonize on and/orinvade through mucosal surfaces.

(a) Requlatable Cassette

A recombinant bacterium of the invention comprises a regulatablecassette. Such a cassette usually comprises a regulatable promoteroperably linked to i) an arginine decarboxylase and an arginine agmatineantiporter; ii) a glutamate decarboxylase and a glutamate/γ-aminobutyricacid antiporter; or iii) a lysine decarboxylase and a lysine/cadaverineantiporter. Each of these elements is described in more detail below.

The term “operably linked,” as used herein, means that expression of anucleic acid sequence is under the control of a promoter with which itis spatially connected. A promoter may be positioned 5′ (upstream) ofthe nucleic acid sequence under its control. The distance between thepromoter and a nucleic acid sequence to be expressed may beapproximately the same as the distance between that promoter and thenative nucleic acid sequence it controls. As is known in the art,variation in this distance may be accommodated without loss of promoterfunction.

A regulatable cassette of the invention may be present in the chromosomeof the recombinant bacterium, or may be present in an extrachromosomalvector. In one embodiment, a regulatable cassette may be present in thechromosome of the recombinant bacterium. Methods of chromosomallyintegrating a regulatable cassette are known in the art and detailed inthe examples. Generally speaking, the regulatable cassette should not beintegrated into a locus that disrupts colonization of the host by therecombinant bacterium, or that negatively impacts the use of thebacterium to evoke an immune response, such as in a vaccine. In oneembodiment, the regulatable cassette may be chromosomally integratedinto the locus that comprises nucleic acid encoding an argininedecarboxylase and/or an arginine agmatine antiporter. In anotherembodiment, the regulatable cassette may be chromosally integrated intothe locus that comprises nucleic acid encoding a glutamate decarboxylaseand/or a glutamate/γ-aminobutyric acid antiporter. In yet anotherembodiment, the regulatable cassette may be chromosomally integratedinto the locus that comprises nucleic acid encoding a lysinedecarboxylase and/or a lysing/cadaverine antiporter.

In another embodiment, a regulatable cassette of the invention may bepresent in an extrachromosomal vector. As used herein, “vector” refersto an autonomously replicating nucleic acid unit. The present inventioncan be practiced with any known type of vector, including viral, cosmid,phasmid, and plasmid vectors. The most preferred type of vector is aplasmid vector.

i) Regulatable Promoter

A regulatable cassette of the invention comprises a regulatablepromoter. As used herein, the term “promoter” may mean a synthetic ornaturally-derived molecule that is capable of conferring, activating orenhancing expression of a nucleic acid. A promoter may comprise one ormore specific transcriptional regulatory sequences to further enhanceexpression and/or to alter the spatial expression and/or temporalexpression of a nucleic acid.

The regulated promoter used herein generally allows transcription of anucleic acid encoding an arginine decarboxylase and a nucleic acidencoding an arginine agmatine antiporter while in a permissiveenvironment (i.e., in vitro aerobic growth), but ceases transcriptionwhile in a non-permissive environment (i.e., during anaerobic growth ofthe bacterium in an animal or human host). For instance, the promotermay be sensitive to a physical or chemical difference between thepermissive and non-permissive environment. Stated another way, aregulated promoter of the invention allows for inducible expression of anucleic acid encoding an arginine decarboxylase and a nucleic acidencoding an arginine agmatine antiporter, even under aerobic conditions.In another embodiment, the regulated promoter used herein generallyallows transcription of a nucleic acid encoding a glutamatedecarboxylase and a nucleic acid encoding a glutamate/γ-aminobutyricacid antiporter while in a permissive environment (i.e., in vitroaerobic growth), but ceases transcription while in a non-permissiveenvironment (i.e., during anaerobic growth of the bacterium in an animalor human host). Stated another way, a regulated promoter of theinvention allows for inducible expression of a nucleic acid encoding aglutamate decarboxylase and a nucleic acid encoding aglutamate/γ-aminobutyric acid antiporter, even under aerobic conditions.In still another embodiment, the regulated promoter used hereingenerally allows transcription of a nucleic acid encoding a lysinedecarboxylase and a nucleic acid encoding a lysine/cadaverine antiporterwhile in a permissive environment (i.e., in vitro aerobic growth), butceases transcription while in a non-permissive environment (i.e., duringanaerobic growth of the bacterium in an animal or human host). Statedanother way, a regulated promoter of the invention allows for inducibleexpression of a nucleic acid encoding a lysine decarboxylase and anucleic acid encoding a lysine/cadaverine antiporter, even under aerobicconditions. Suitable examples of such regulatable promoters are known inthe art.

In some embodiments, the promoter may be responsive to the level ofarabinose in the environment. Generally speaking, arabinose may bepresent during the in vitro growth of a bacterium, while typicallyabsent from host tissue. In one embodiment, the promoter is derived froman araC-P_(BAD) system. The araC-P_(BAD) system is a tightly regulatedexpression system, which has been shown to work as a strong promoterinduced by the addition of low levels of arabinose. The araC-araBADpromoter is a bidirectional promoter controlling expression of thearaBAD nucleic acid sequences in one direction, and the araC nucleicacid sequence in the other direction. For convenience, the portion ofthe araC-araBAD promoter that mediates expression of the araBAD nucleicacid sequences, and which is controlled by the araC nucleic acidsequence product, is referred to herein as P_(BAD). For use as describedherein, a cassette with the araC nucleic acid sequence and thearaC-araBAD promoter may be used. This cassette is referred to herein asaraC-P_(BAD). The AraC protein is both a positive and negative regulatorof P_(BAD). In the presence of arabinose, the AraC protein is a positiveregulatory element that allows expression from P_(BAD). In the absenceof arabinose, the AraC protein represses expression from P_(BAD). Thiscan lead to a 1,200-fold difference in the level of expression fromP_(BAD).

Other enteric bacteria contain arabinose regulatory systems homologousto the araC-araBAD system from E. coli. For example, there is homologyat the amino acid sequence level between the E. coli and the S.Typhimurium AraC proteins, and less homology at the DNA level. However,there is high specificity in the activity of the AraC proteins. Forexample, the E. coli AraC protein activates only E. coli P_(BAD) (in thepresence of arabinose) and not S. Typhimurium P_(BAD). Thus, anarabinose regulated promoter may be used in a recombinant bacterium thatpossesses a similar arabinose operon, without substantial interferencebetween the two, if the promoter and the operon are derived from twodifferent species of bacteria.

Generally speaking, the concentration of arabinose necessary to induceexpression is typically less than about 2%. In some embodiments, theconcentration is less than about 1.5%, 1%, 0.5%, 0.2%, 0.1%, or 0.05%.In other embodiments, the concentration is 0.05% or below, e.g. about0.04%, 0.03%, 0.02%, or 0.01%. In an exemplary embodiment, theconcentration is about 0.05%.

In other embodiments, the promoter may be responsive to the level ofmaltose in the environment. Generally speaking, maltose may be presentduring the in vitro growth of a bacterium, while typically absent fromhost tissue. The malT nucleic acid sequence encodes MalT, a positiveregulator of four maltose-responsive promoters (P_(PQ), P_(EFG),P_(KBM), and P_(S)). The combination of malT and a mal promoter createsa tightly regulated expression system that has been shown to work as astrong promoter induced by the addition of maltose. Unlike thearaC-P_(BAD) system, malT is expressed from a promoter (P_(T))functionally unconnected to the other mal promoters. P_(T) is notregulated by MalT. The malEFG-malKBM promoter is a bidirectionalpromoter controlling expression of the malKBM nucleic acid sequences inone direction, and the malEFG nucleic acid sequences in the otherdirection. For convenience, the portion of the malEFG-malKBM promoterthat mediates expression of the malKBM nucleic acid sequence, and whichis controlled by the malT nucleic acid sequence product, is referred toherein as P_(KBM), and the portion of the malEFG-malKBM promoter thatmediates expression of the malEFG nucleic acid sequence, and that iscontrolled by the malT nucleic acid sequence product, is referred toherein as P_(EFG). Full induction of P_(KBM) requires the presence ofthe MalT binding sites of P_(EFG). For use in the vectors and systemsdescribed herein, a cassette with the malT nucleic acid sequence and oneof the mal promoters may be used. This cassette is referred to herein asmalT-P_(mal). In the presence of maltose, the MalT protein is a positiveregulatory element that allows expression from P_(mal).

In still other embodiments, the promoter may be sensitive to the levelof rhamnose in the environment. Analogous to the araC-P_(BAD) systemdescribed above, the rhaRS-P_(rhaB) activator-promoter system is tightlyregulated by rhamnose. Expression from the rhamnose promoter (P_(rha))is induced to high levels by the addition of rhamnose, which is commonin bacteria but rarely found in host tissues. The nucleic acid sequencesrhaBAD are organized in one operon that is controlled by the P_(rhaBAD)promoter. This promoter is regulated by two activators, RhaS and RhaR,and the corresponding nucleic acid sequences belong to two transcriptionunits that are located in the opposite direction of the rhaBAD nucleicacid sequences. If L-rhamnose is available, RhaR binds to the P_(rhaRS)promoter and activates the production of RhaR and

RhaS. RhaS together with L-rhamnose in turn binds to the P_(rhaBAD) andthe P_(rhaT) promoter and activates the transcription of the structuralnucleic acid sequences. Full induction of rhaBAD transcription alsorequires binding of the Crp-cAMP complex, which is a key regulator ofcatabolite repression.

Generally speaking, the concentration of rhamnose necessary to induceexpression is typically less than about 2%. In some embodiments, theconcentration is less than about 1.5%, 1%, 0.5%, 0.2%, 0.1%, or 0.05%.In other embodiments, the concentration is about 0.6%, about 0.5%, about0.4%, about 0.3%, about 0.2%, or about 0.1%. In an exemplary embodiment,the concentration is about 0.1%. In another exemplary embodiment, theconcentration is about 0.4%

Although both L-arabinose and L-rhamnose act directly as inducers forexpression of regulons for their catabolism, important differences existin regard to the regulatory mechanisms. L-Arabinose acts as an inducerwith the activator AraC in the positive control of the arabinoseregulon. However, the L-rhamnose regulon is subject to a regulatorycascade; it is therefore subject to even tighter control than the araCP_(BAD) system. L-Rhamnose acts as an inducer with the activator RhaRfor synthesis of RhaS, which in turn acts as an activator in thepositive control of the rhamnose regulon. In the present invention,rhamnose may be used to interact with the RhaR protein and then the RhaSprotein may activate transcription of a nucleic acid sequenceoperably-linked to the P_(rhaBAD) promoter. In some embodiments, therhaRS-P_(rhaB) activator-promoter cassette from an E. coli K-12 strainmay be used.

In still other embodiments, the promoter may be sensitive to the levelof xylose in the environment. The xylR-P_(xylA) system is anotherwell-established inducible activator-promoter system. Xylose inducesxylose-specific operons (xylE, xylFGHR, and xylAB) regulated by XylR andthe cyclic AMP-Crp system. The XylR protein serves as a positiveregulator by binding to two distinct regions of the xyl nucleic acidsequence promoters. As with the araC-P_(BAD) system described above, thexylR-P_(xylAB) and/or xylR-P_(xylFGH) regulatory systems may be used inthe present invention. In these embodiments, xylR P_(xylAB) xyloseinteracting with the XylR protein activates transcription of nucleicacid sequences operably-linked to either of the two P_(xyl) promoters.

The nucleic acid sequences of the promoters detailed herein are known inthe art, and methods of operably-linking them to a nucleic acid sequenceencoding an arginine decarboxylase and a nucleic acid encoding anarginine agmatine antiporter are known in the art and detailed in theexamples.

ii) A Nucleic Acid Sequence Encoding an Arginine Decarboxylase

A regulatable cassette of the invention further comprises an argininedecarboxylase. An arginine decarboxylase is an enzyme that catalyzes thechemical reaction L-arginine

agmatine and CO₂, and is classified as EC 4.1.1.19. Generally speaking,an arginine decarboxylase useful in the present invention will haveacitivity similar to AdiA (e.g. protect a cell from low pH). Suitableexamples of arginine decarboxylase are known in the art, and may includethe following enzymes (referenced by UNIPROT identifiers, available atwww.uniprot.org): Q5L5E7, AAXB_CHLAB; Q822F3, AAXB_CHLCV; Q255I0,AAXB_CHLFF; Q9PK21, AAXB_CHLMU; Q9Z6M7, AAXB_CHLPN; P0C8R4, AAXB_CHLT2;Q3KLY3, AAXB_CHLTA; P0C8R5, AAXB_CHLTB; O84378, AAXB_CHLTR; Q7XRA1,ADC2_ORYSJ; Q96A70, ADC_HUMAN; P28629, ADIA_ECOLI; Q9YG22, ARGDC_AERPE;A8MBV3, ARGDC_CALMQ; A2BM05, ARGDC_HYPBU; A8AAB6, ARGDC_IGNH4; A4YH98,ARGDC_METS5; Q8ZWK3, ARGDC_PYRAE; A4WIW6, ARGDC_PYRAR; A3MTU5,ARGDC_PYRCJ; A1RV83, ARGDC_PYRIL; B1YD10, ARGDC_PYRNV; A3DLU8,ARGDC_STAMF; Q4J932, ARGDC_SULAC; C3N6F7, ARGDC_SULIA; C4KHX2,ARGDC_SULIK; C3MQN7, ARGDC_SULIL; C3MWN7, ARGDC_SULIM; C3NGS9,ARGDC_SULIN; C3NEW5, ARGDC_SULIY; Q9UWU1, ARGDC_SULSO; Q971 K9,ARGDC_SULTO; O27983, PDAD1_ARCFU; Q8TLM4, PDAD1_METAC; P58889,PDAD1_METMA; O30240, PDAD2_ARCFU; Q8TKB4, PDAD2_METAC; P58890,PDAD2_METMA; B3EGI2, PDAD_CHLL2; B3QM53, PDAD_CHLP8; B3ELD9, PDAD_CHLPB;B3QWJ5, PDAD_CHLT3; Q8KEX0, PDAD_CHLTE; B0R6U7, PDAD_HALS3; Q9HNQ0,PDAD_HALSA; A6UUL7, PDAD_META3; Q12UX3, PDAD_METBU; Q57764, PDAD_METJA;Q8TXD4, PDAD_METKA; A4G0Z0, PDAD_METM5; A9A979, PDAD_METM6; A6VHH0,PDAD_METM7; Q6LWX2, PDAD_METMP; O26956, PDAD_METTH; A6UQM7, PDAD_METVS;A9A5S1, PDAD_NITMS; Q3B5D1, PDAD_PELLD; Q6KZS5, PDAD_PICTO; B4S6J7,PDAD_PROA2; A4SFG2, PDAD_PROVI; Q9V173, PDAD_PYRAB; Q8U0G6, PDAD_PYRFU;O59240, PDAD_PYRHO; Q5JFI4, PDAD PYRKO; Q9HK30, PDAD_THEAC; C6A2R5,PDAD_THESM; Q97AN7, PDAD_THEVO; Q0W1C7, or PDAD_UNCMA.

In some embodiments, an arginine decarboxylase of the invention is froma Salmonella species. In particular embodiments, an argininedecarboxylase of the invention is from a Salmonella Typhi strain. Instill other embodiments, an arginine decarboxylase of the invention isfrom a S. Typhi Ty2 strain. In an exemplary embodiment, an argininedecarboxylase of the invention has the amino acid sequence of theprotein at accession number Q8Z1 P1.

iii) A Nucleic Acid Encoding an Arginine Agmatine Antiporter

A regulatable cassette of the invention comprises an arginine agmatineantiporter. An arginine agmatine antiporter exchanges extracellulararginine for its intracellular decarboxylation product agmatine (Agm)thereby expelling intracellular protons. Generally speaking, an arginineagmatine antiporter useful in the present invention will have activitysimilar to AdiC (e.g. protect a cell from low pH). Suitable examples ofa arginine agmatine antiporter are known in the art, and may include thefollowing enzymes (referenced by UNIPROT identifiers, available atwww.uniprot.org):

Q5L5E6 Q822F2 Q255I1 Q9PK20 Q9Z6M8 B0B7U3 Q3KLY0 B0BC08 O84379 P60063P60062 P60061 P60065 P60066 P60064 Q8ZGS9 F9I2W4 L0ZZ71 K5SRC8 L2XUK4L0ZZ90 L3LBG0 K3L3A1 I7RFE4 K5JIM6 H4VPM7 K3ECI9 K5JII2 L4W4Y5 H4VPK5F3NW25 K3B3S5 I7V0V1 K3SS41 K5U1P0 L4F2K6 L5IZK9 L4VBA1 E1IV59 L8T7H9E1IV81 I6FGU1 L8RFY1 J1FC03 I5XD20 F1ZQN0 L3RY40 L4T3H6 L4T549 B3H9N6L0X6N1 L0X6Q1 B5NPC3 B5MPV9 I6JZL9 I7UDX0 A9ZUE1 L1GKB6 L4YQS8 I2SQ31B5PIR2 L2AD21 B3YHW3 F9A052 G1ZS25 I6I720 L3ANK2 I8L5B5 I7V0M1 B2P2P0I6K2D0 D1TQ94 B3XCN3 L4TIY7 E7UJV3 G7AK02 I2ZAI5 I5DC16 F5MWJ7 K5U1M6L3XAL9 L5DBB6 C0AU61 I8AEV7 I7S457 J9XI24 C0AU59 C0AU62 F4UGH3 L9HFX9I5XWG2 L3EKM3 L3VWN3 L3DTY3 K3RCT8 L8CSG7 I5VI26 K2X636 L2E4E2 K3AGX2I7UAZ0 L1ZHH6 L3M033 D7ZE63 I5D8I3 I7X7J6 I5Q9Q8 I5M3V3 J1YF14 D7ZE41L2ZZ90 L2ZV57 L4FNN9 L1R3X9 L1R3Z5 L3YQ74 D8AX24 J9XD49 D8AX02 L3BVT4L2Y3Z0 L3AQT2 K3L9D5 I5S6B5 D2ZGU0 H4W4R4 L3IJA7 L4JLJ2 K2ZXC3 I8BDE6H4W4P4 D6KD06 L4A9N4 G5RNX8 I4JEM2 K2ZDJ2 D8AKJ4 L3XEU2 I8P6H8 E7K6V9L8Z8R4 L8YKJ3 D8AKL7 L3NNJ6 L3BFQ8 K3MKD0 H4KAZ1 H4KAX3 L4IHB5 L2BF09E7V2M9 G9WDQ0 F1Y6E3 K3JZ37 L2BX70 J9X347 B3IGV7 L4CV86 K5SPP8 L8BQC1L3NN06 K3U457 F4T7G8 E3Y474 B3AHE0 L4H192 E9TP44 I6G8F1 I6GL91 I6GBL6L8YEL4 E9TP22 G7B431 E9U4M4 I6GBF5 I6F968 L0X7G9 L0X7I9 K3QB35 I5EN09L1GNR1 L1GNP4 K5QU54 L4ZG30 J1W870 I7XHW6 G5WM30 L2WZD7 L1AB99 L1AB78I7V7C5 G5NFS9 I8NA30 G1YHG9 G5NFT1 E3XKM9 L1EFJ6 L4QDY7 L1EFL8 K2W2K4F4V9D8 G2CT24 I7PI89 C8T226 I5W5W6 B5P6C4 H5N2D9 L4EP61 I5HRC9 H5N267I7UST4 L1F849 L1F871 K5T2Y1 E7JIF7 F5QPJ9 H4WZP7 L3RSY3 H4WZM8 I2R8G7B5Q4D3 I5MJT7 L8C1L1 I2UGJ6 F3VDW4 H1FJ08 G5MRE2 I5MTW8 G5MRE4 K3KCA8L4XNM3 K5DXC6 K5ISM6 K5F1V1 K5ISH8 I8AKN2 I6CMX1 G7A768 G0F4S0 E6B426J1C6G7 L4SYQ4 K3S724 I8H5G7 J5CMZ3 I5M6S7 J1W394 L4KR23 I6BD24 K3GSB1L4UGY3 B2NQU7 E9TK06 E9TK28 I2ZLX4 F5QBC2 I5D999 B0GR46 D8C1N4 D8BQX0L3IMN2 E5ZS94 L2X415 B3WYW2 E5ZSB7 L8SVA7 L3MX95 D7ZVD8 I7ZAY6 F9ALT1I5S787 K2XVU7 H1DRT2 G5U5M4 I5EVB1 I8SH69 G9Y8K8 H1E1A5 G9Y4C6 G9Y9L2L8SLE6 I3A6R7 G9Y813 E7TTL9 I2T1Y1 J1GHD8 G5X1P1 L1BFR5 L1BFT3 G5UZS2F9C3H2 G5QBN3 I5G8K3 L1BCM1 L1BCJ8 K2V6L4 G9SB43 B0GG51 L2CSK5 L5D1W2J1EY15 G5VHH0 G2CCI8 K3GZI0 E1HK03 K3PN87 L4XCP6 I6DUZ6 I6EXQ7 I5QHY5E1HJY3 D4E2F3 G5LHQ4 L3CJQ8 L2UQB9 L3FKD7 K3TEP7 L9EA37 I6DE79 F3WRA4I2V7B6 L0YSU5 K5I296 L0YQH4 L2AJI5 F4LZD4 G2B2X5 G0DBW7 L3MTD6 I8IDI1I6IKD0 K3ADY5 L5AR67 L4ZY81 I5Z6K3 B3BTH9 G5SJZ9 B0HEW5 G5QT01 B2N252K3J5D8 I5IS05 E7JBV5 L3NM54 K5HAC9 L4PPI9 K5J592 E1JCI2 L4TRI3 L5C0A6D4F0D4 D4F4Y3 D4F2I3 E1JCG1 I7SA11 I6KTI0 J9XCX8 D4F0F6 K3HBW8 L4YWU8L2UUC4 I2RRR4 K5SHK1 H4USI6 L3SMZ0 I2TWS7 I7UER9 I7RDJ7 F3W5J5 G6ZAS1H4USG6 H4YPM0 L5HV94 H4YPH3 I5QW95 I7WAW3 A9Z9Y2 E9U9I3 L1CQU5 L4QRV7L4TFJ6 D7YA60 L1CQW4 I2SBG7 L8S2L4 J5XTX4 H4Z4M5 E9U9G3 D7YA80 K3R0A0K3DX62 L3ZGY3 L3KR37 G5PW35 K2V9Y3 B2PJH9 I7W0J5 G5PW33 G5PGS6 L3GF20L5EKI8 K5GG82 L5BZY9 L1KR74 K3C1C8 L3H308 D8E3L6 C4U4Q1 I2XLP9 I5WJG5D8E3J4 H6P1D1 L3VT02 L5GSI7 I5TR12 J1LTN0 L4NC45 G5VX93 L9BGL3 I7WXF3I5J6Y3 L9IJ71 L2VEC8 J9WRB0 I5S9Y5 G1YK68 H3KCD0 I5V8Q8 L9HX28 L4L951L1VUB5 L4AJL2 I6HT62 I5HAV4 I5U539 I7P7U1 L9ERL8 G2D7C4 L4I9E1 M3V1I3H5JRD7 K5G7H8 K5FEJ8 L9AVL2 I5XA14 F5MT32 I7W894 H5JRS9 L1BGE1 L1BGG3K3GB62 F8YV39 B1EQG3 J1NUH4 L2XN23 I6CJ09 F4UWB4 I6CSL5 J1ZYA9 L1ED04L4T2N7 L3EV49 L1EE45 F5PH59 K2VYG0 L5A3N0 L3I4F5 L1FUJ6 L5EEA8 L1FUB8K3I8N8 L5EBV4 L4MLC0 L3SMU3 G5R8V8 L1WZ84 D7YJ24 L4SIF7 B3BAY7 I7QIR7D7YJ03 I6E3S5 I6E2M6 L1FFZ9 L1FHA6 L3XNJ9 L3AIS0 L3DCM3 L2ZQW7 G9Z382G9Z6T2 F9B733 L3CTW1 K5GGB1 K5GGC9 L3RU66 K5V7V7 B5CDU5 K2W084 L3R3T7L3H2Z3 I5KPM2 G5WDR4 I8HN84 K2XEQ7 J1XSN7 L4B207 J2LYB6 L9EWN3 H7E8B6H7EFP3 G2BH56 I7TE46 G5N5X9 I2VCV4 K3R9D1 K3U183 L4RNN6 L3FZ43 G5XKR7F8Z5T6 K5SMQ6 L4NUX8 H5HFY0 L5FEK0 K3F8X8 H5HFW1 I7PQR4 L3LTC8 L4A672G5NWE6 I2Y4M6 G5UG24 E7THT7 J9WX42 G5NWE4 K3DHG1 L4YF33 K5ERV4 L4IQR3L3J974 K5ERT7 C4UFE9 F9AC54 J1EAB4 F3QA56 L3PA82 L4WDV5 L3CZZ0 K3MPZ0J2LWC7 I7Q7C5 I8QBE8 I5L1L1 L8DAI2 L3WLQ1 I5SND2 L8T8F8 E7T215 I7W989L8QUU4 L4BBX6 L5C5U6 E2KBB2 L9B483 L9G1R7 L0Z001 L4RL04 L0YXM5 E2X4N1L9FCW5 G5Y4V3 H1ENB2 L5AT29 K2Z1I4 F7N4C2 E7UCF3 I8HE83 K2XZX6 H1F466G6Z285 I5KRA0 F7N4C1 L4KGB0 M1SKM5 L4QZX7 M1RQ73 F5P3T9 L4CN89 L4V0U9L3U4Y7 I5JAK7 I7WZT3 G7C0I5 F8XI69 K3FB12 L3K5K6 I6FQ39 F8ZRQ5 I6FQG6I2VUS4 F8X8V9 K2XJA0 L5E756 L4F8M8 L3ZJ80 K5H5J8 L1ZPU4 F9AYU6 F4QX28H4UB16 L4I150 L2DP62 B5PY28 H4UD30 L9CGU3 I6CE72 L1WYU6 L3Q752 E1I8N2I0A439 I2YEN5 E1I8Q3 I2XF31 L2B6G5 L4DSI6 I2X267 K2UME8 L9HY73 G5S484L9G6W1 G5RY80 L5J565 L3UUU8 L4C5Y5 L4MNW4 L4DPM8 L3U3J6 L4A9T1 L8RSC0B6ZV29 L8SCJ8 L3L740 L5D6D0 K3CQ23 I6BGH7 I6KUL9 F4VPI9 J1P1K1 G6ZP97B5MYN3 D8BNH2 L0XFR8 E6AW46 E6BPS4 K3EY17 L0XFT6 L1DUJ6 L1DUH5 E9A511E6AW24 E9A9Z5 E6BPQ3 I5PCC2 D8BNF2 D8BKR1 M1YQ20 M1YQL5 H5HXX1 L5FNP9D8EPN7 L4J9M5 G1ZD77 H5HXV2 I5FZI4 G5MBY2 D8EPL5 F1XKZ5 L3R5N4 I2PFB7K3CLI6 I8GHM8 G5YAK0 I5Z8Y0 L0YEQ2 L5GS53 L0YFU2 L2Z6T1 I7YZ57 J1GJF9K3SPI8 L1R4J3 L1R4N9 B0H3G9 L8R4H6 D0YZT1 L8ZV52 E2KS00 G7ATI2 B3I3F2I7NQ44 L4FPP1 L1YEC5 L3G7A2 L4PN37 E2JZ15 G7BEV7 L2CG18 K6BMP2 K3IBQ9L4NAX4 L4UVT9 L1YFF5 K6AQQ4 E7SMJ3 H4LD96 I5TK17 K2YQG0 B5N8X1 D4BKK1H4LD94 L1ZB17 L5FGA8 L2VPB6 I5UWQ2 G7BSL0 K2W4M5 G2A7N1 I8ABI5 E6A679L3EMC4 B5BW09 J1EEU3 J9XAE9 G2BXS5 L8ZU36 I2RDZ7 E6A6A0 L5BAV4 L1D8C7L1D8A4 F9BI15 L9GKG1 G5TR25 I5GHK7 E7IWX0 L5HY14 K3BUT3 I5JSB7 I5PZ94L4HCK1 L9DIV7 B0HU12 I8R9N2 F9BVG9 B4AA00 J9WX07 D7Z320 L3W464 L4WBE5D7XTM6 L1VQ23 D7XTK5 D7Z341 I5YHQ1 F4VMA3 K3MDC6 F5NAH0 K3KB42 L9AF12L4DM02 L1X3N5 H5ISJ7 B3A6E6 I2DXM6 I6D2V7 I6D2V9 H1BTG9 H5ISL6 I2WGN2I6D2W0 I6CR58 K5FVW8 K5HMA4 K5HM79 I7TD77 I2Z670 I5EQF3 K2T9K2 I7Z9Z3I6J638 F8ZDV2 L9CEA9 B3B061 E7HSW8 K3MX00 F4TP19 K2V813 L4K1S5 L3PUI4H4J2D2 G2AP22 H4J2B4 E7IDB4 E2X267 F5PWY4 J9X778 D8CBL7 L1Y967 L4KWW5L0ZZ14 L0ZZ44 D7X582 L4XFS7 L3UDG0 L4EEY0 D8CBN6 I5NVZ9 I2TLP7 D7X560L5HPI1 H5IBZ7 L2WC77 I6J919 L9CH33 H5IBX8 J1LJU9 I5HMY4 L2D672 L4QAI1L1CM27 L3PH92 L1CMJ2 L2TZ71 L9DKJ3 F4U276 K2W210 C4S0N7 L4MQ21 L3YTD0K3GPD1 K3NAF9 G6ZZN4 J1D607 L2VLJ7 L5GJS3 K3P2I6 L1VS42 L3ITJ5 D8AFI1D8AFF8 D8AFF9 B3HVQ4 F4SSI1 L4GNN4 L3UXG7 G4C9J0 E7HCX1 G4C3K1 C3SGT2C6ED09 A9ANX5 B1LQD3 A4JQ30 B7NG51 G8W1Q4 B4TED3 B7MSM8 D2TNK2 A9R299D3GTZ4 B4TS79 B5F2H0 D2ADB4 B7M8M5 Q399G7 E1WEY4 B2TXC1 Q0B7H7 B7NSS7B7LB57 B4T2J5 E3PD34 A8A7L1 F8L8H9 F8L8H8 B5Z2C3 A7ZUY5 E8P6N2 B5FRG8E8P6N3 A7FKG8 B7MJY9

In some embodiments, an arginine agmatine antiporter of the invention isfrom a Salmonella species. In particular embodiments, an arginineagmatine antiporter of the invention is from a Salmonella Typhi strain.In still other embodiments, an arginine agmatine antiporter of theinvention is from a S. Typhi Ty2 strain. In an exemplary embodiment, anarginine agmatine antiporter of the invention has the amino acidsequence of the protein at accession number P60065.

In certain embodiments of the invention the nucleic acid encoding anarginine agmatine antiporter is fused with an arginine decarboxylaseencoding sequence such that the intervening regulatory gene adiY isdeleted. For instance, in certain embodiments, a Salmonella adiAsequence is fused to a Salmonella adiC sequence.

iv) A Nucleic Acid Encoding a Glutamate Decarboxylase

In some embodiments, a regulatable cassette may comprise a glutamatedecarboxylase. A glutamate decarboxylase is an enzyme that catalyzes thechemical reaction L-glutamate

γ-aminobutyric acid (GABA) and CO₂, and is classified as EC 4.1.1.15.Generally speaking, a glutamate decarboxylase useful in the presentinvention will have activity similar to GadA and/or GadB (e.g. protect acell from low pH). Suitable examples of glutamate decarboxylase areknown in the art, and may include the following enzymes (referenced byUNIPROT identifiers, available at www.uniprot.org): GadB—P69910, O0418,Q928R9, P69909, P69912; GadA—P69908, Q83QR1, P58288, P69912, or Q9F5P3.

In some embodiments, a glutamate decarboxylase of the invention is fromEscherichia coli. In particular embodiments, a glutamate decarboxylaseof the invention is from an Escherichia coli O157 strain. In still otherembodiments, a glutamate decarboxylase of the invention is from aShigella species. In some embodiments, two glutamate decarboxylases maybe present in the same strain (GadA and GadB). In an exemplaryembodiment, a glutamate decarboxylase of the invention has the aminoacid sequence of P69910.

v) A Nucleic Acid Encoding a Glutamate/γ-aminobutyric Acid Antiporter

In other embodiments, a regulatable cassette of the invention maycomprise a glutamate/γ-aminobutyric acid antiporter. Aglutamate/γ-aminobutyric acid antiporter exchanges extracellularglutamate for its intracellular decarboxylation product/γ-aminobutyricacid thereby expelling intracellular protons. Generally speaking, aglutamate/γ-aminobutyric acid antiporter useful in the present inventionwill have activity similar to GadC (e.g. protect a cell from low pH).Suitable examples of a glutamate/γ-aminobutyric acid antiporter areknown in the art, and may include the following enzymes (referenced byUNIPROT identifiers, available at www.uniprot.org): C8U8G2, C6UU78,P58229, P63235, Q8FHG6, EOJ6C9, C9QVX6, Q9CG19, O30417, C7LH11, Q8YBJ1,Q577E9, C4PPM2, B1LFC4, BOBBJ6, B7LZ92, B7L7J1, B6J3P9, Q03U70, A8A049,B0B9W6, E1P9D3, Q3KME6, D5D2L2, C8U8G2, or B7LRF2.

In some embodiments, a glutamate/γ-aminobutyric acid antiporter of theinvention may be from Escherichia coli. In particular embodiments, aglutamate/γ-aminobutyric acid antiporter of the invention is from anEscherichia coli O157 strain. In still other embodiments, aglutamate/γ-aminobutyric acid antiporter of the invention is from aShigella species. In an exemplary embodiment, a glutamate/γ-aminobutyricacid antiporter of the invention has the amino acid sequence of aprotein with accession number C6UU78.

vi) A Nucleic Acid Encoding a Lysine Decarboxylase

In certain embodiments, a regulatable cassette of the invention furthercomprises a lysine decarboxylase. A lysine decarboxylase is an enzymethat catalyzes the chemical reaction L-lysine

cadaverine and CO₂, and is classified as EC 4.1.1.18. Generallyspeaking, a lysine decarboxylase useful in the present invention willhave activity similar to CadA (e.g. protect a cell from low pH).Suitable examples of lysine decarboxylase are known in the art, and mayinclude the following enzymes (referenced by UNIPROT identifiers,available at www.uniprot.org): P0A1Z1, Q8X8X4, P0A9H4, or C5A1C4.

In some embodiments, a lysine decarboxylase of the invention is from aSalmonella species. In particular embodiments, a glutamate decarboxylaseof the invention is from Salmonella Typhi. In other embodiments a lysinedecarboxylase of the invention is from an Escherichia coli strain. In anexemplary embodiment, a lysine decarboxylase of the invention has theamino acid sequence of P0A1Z1.

vii) A Nucleic Acid Encoding a Lysine/Cadaverine Antiporter

A regulatable cassette of the invention comprises lysine/cadaverineantiporter. A lysine/cadaverine antiporter exchanges extracellularlysine for its intracellular decarboxylation product cadaverine therebyexpelling intracellular protons. Generally speaking, a lysine/cadaverineantiporter useful in the present invention will have activity similar toCadB (e.g. protect a cell from low pH). Suitable examples of alysine/cadaverine antiporter are known in the art, and may include thefollowing enzymes (referenced by UNIPROT identifiers, available atwww.uniprot.org): Q8Z4M1, P0AAF0, P0AAE8, J9ZST9, K0AT87, K0BD30,D3QL54, Q5PIH7, or B5QTS6.

In some embodiments, a lysine/cadaverine antiporter of the invention isfrom Salmonella species. In particular embodiments, a lysine/cadaverineantiporter of the invention is from Salmonella Typhi. In otherembodiments a lysine/cadaverine antiporter of the invention is fromEscherichia coll. In an exemplary embodiment, a lysine/cadaverineantiporter of the invention has the amino acid sequence of Q8Z4M1.

viii) A Nucleic Acid Encoding a Chloride Channel

In some embodiments, a regulatable cassette of the invention comprises achloride channel protein. A chloride channel prevents membranehyperpolarization at low pH. Generally speaking, a chloride channelprotein useful in the present invention will have activity similar toClcA from E. coll. Suitable examples of a chloride channel are known inthe art, and may include the following (referenced by UNIPROTidentifiers, available at www.uniprot.org): P37019, Q3Z5K2, Q8ZBM0, Q1RG33, B7LWB6, B5Y1 L4, Q325Y4, Q32JV3, Q0T851, P59639, A5F0D5, Q9KM62,C3LVE3, Q87GZ9, Q7MDF0, A7FM08, Q1C3X2, A9R1 E4, Q1CLU6, B1IQI5, A6T4V9,B2U300, A7N6K9, Q8D6J0, B2K549, A4TPW7, B1JK21.

In some embodiments, a chloride channel of the invention is fromEscherichia species. In particular embodiments, a chloride channel ofthe invention is from E coli. In other embodiments, a chloride channelof the invention is has significant homology with the E. coli chloridechannel, ClcA. A skilled artisan would be able to identify thoseproteins with significant homology to an E. coli chloride channel. In anexemplary embodiment, the chloride channel of the invention has theamino acid sequence of P37019.

ix) Nucleic Acids Encoding a Urease System

In some embodiments, a regulatable cassette of the invention comprisesall or some of a Ni-dependent urease system. A Ni-dependent ureasesystem enables survival in extremely low pH by acid acclimation.Generally speaking, a Ni-dependent urease system useful in the presentinvention has activity similar to the Helicobacter pylori Ni-dependenturease system. The regulatable cassette may comprise urease proteins,such as UreA and UreB, and a carbonic anhydrase, such as HP1186.Additional components of the urease system, such as a proton-gated ureachannel (UreI) and a chaperone complex necessary to incorporate Ni ionsinto the urease apoenzyme (UreE, UreF, UreG, UreH) may be under controlof a constitutive promoter. Constitutive promoters are known in the artand may include P_(Ipp).

In some embodiments, a Ni-dependent urease system of the invention isfrom Helicobacter species. In an exemplary embodiment, the Ni-dependenturease system of the invention is from H. pylori.

x) Transcription Termination Sequence

In some embodiments, the regulatable cassette further comprises atranscription termination sequence. A transcription termination sequencemay be included to prevent inappropriate expression of nucleic acidsequences adjacent to the cassette.

(b) Acid Sensitive/Increase in Acid Resistance

In some embodiments, a recombinant bacterium of the invention is acidsensitive. As used herein, “acid sensitive” means that when cells arecultured under aerobic conditions in minimal media and in the absence ofinduction of the regulatable cassette, less than 1% of the bacteria areviable after 4 hours at pH3.

In some embodiments, the bacterium may be acid sensitive due to a lossof function of the acid tolerance response. In other embodiments, thebacterium may be acid sensitive due to loss of function of an acidresistance system such as the arginine decarboxylase or lysinedecarboxylase system. Such “loss of function” may be caused by one ormore mutations in the acid tolerance response, the argininedecarboxylase acid resistance system, the lysine decarboxylase system,or related systems that result in acid sensitivity. In an alternativeembodiment, the bacterium may contain no mutation, but be acid sensitivedue to exposure to environmental conditions that repress or fail toinduce the acid tolerance or acid resistance systems.

In one embodiment, the bacterium may be acid sensitive, at least inpart, because of an rpoS mutation. In another embodiment, the bacteriummay be acid sensitive, at least in part, because of a phoPQ mutation. Instill another embodiment, the bacterium may be acid sensitive, at leastin part, because of a fur mutation. In still yet another embodiment, thebacterium may be acid sensitive, at least in part, because of a guaBAmutation.

Advantageously, an acid sensitive bacterium of the invention increasesits acid resistance when the regulatable promoter is induced. As usedherein “an increase in acid resistance” means that after induction ofthe regulatable cassette, when cells are cultured under aerobicconditions in minimal media and challenged at pH 3.0 for 4 hours, thenumber of viable bacteria after 4 hours is increased >10-fold comparedto the parent strain lacking the acid resistance system. In someembodiments, induction of the regulatable promoter results in the samedegree of acid resistance as the wild-type strain (e.g. without amutation(s) that confers acid sensitivity). In other embodiments,induction of the regulatable promoter results in a greater degree ofacid resistance than the wild-type strain.

(c) Other Mutations

A bacterium of the invention may comprise one or more mutationsdesirable in a bacterium used to evoke an immune response, such as in avaccine. In particular, a bacterium may comprise one or more mutationsto increase invasiveness, one or more mutations to allow endosomalescape, one or more mutations to reduce bacterium-induced hostprogrammed cell death, one or more mutations to induce lysis of thebacterium, one or more mutations to express a nucleic acid encoding anantigen, one or more mutations to attenuate the bacterium, and/or othermutations to enhance the performance of the bacterium as a vaccine.

(d) Exemplary Embodiments

In exemplary embodiments of the present invention, the recombinantbacterium is a Salmonella Typhi bacterium adapted for use as a liveattenuated vaccine. In further exemplary embodiments, the argininedecarboxylase and the arginine agmatine antiporter comprising theregulatable cassette are derived from a Salmonella bacterium. In stillfurther exemplary embodiments, the arginine decarboxylase and thearginine agmatine antiporter comprising the regulatable cassette areadiA and adiC from Salmonella Typhi. In some embodiments, the cicA genefrom E. coli is present in the chromosome and transcribed from its ownnative promoter, a heterologous constitutive promoter or a heterologousregulatable promoter.

In still another embodiment, a recombinant bacterium of the inventionmay comprise a mutation in at least one of aroD, guaBA, rpoS, fur, orphoPQ. In some embodiments, the regulatable acid resistance cassette isregulated by a sugar-inducible promoter. The recombinant bacterium isacid sensitive in the absence of inducer for the regulatable acidresistance cassette. In particular embodiments, the regulatory promoteris responsive to the presence of rhamnose or arabinose. In someembodiments, the acid resistance mechanism comprises a ΔP_(cadBA):TTrhaSR P_(rhaBAD) cadBA or ΔP_(cadBA)::TT araC P_(araBAD) cadBA mutation.

In further exemplary embodiments, the lysine decarboxylase and thelysine: cadaverine antiporter comprising the regulatable cassette arederived from a member of the y-proteobacteria class. In other exemplaryembodiments, the lysine decarboxylase and the lysine: cadaverineantiporter are cadA and cadB from Salmonella. In still further exemplaryembodiments, cadA and cadB are derived from Salmonella Typhi. In someembodiments, the cicA gene from E. coli is present in the chromosome andtranscribed from its own native promoter, a heterologous constitutivepromoter or a heterologous regulatable promoter.

In a different exemplary embodiment, the regulatable acid resistancecassette is regulated by a sugar-inducible promoter. The recombinantbacterium is acid sensitive in the absence of inducer for theregulateable acid resistance cassette. In particular embodiments, thepromoter is responsive to the presence of rhamnose or arabinose. Infurther exemplary embodiments, the glutamate decarboxylase and theglutamate/γ-aminobutyric acid antiporter comprising the regulatablecassette are derived from a bacterium of the y-proteobacteria class. Instill further exemplary embodiments, the glutamate decarboxylase and theglutamate/γ-aminobutyric acid antiporter comprising the regulatablecassette are from Escherichia coli. In particular embodiments, aglutamate decarboxylase of the invention is from an Escherichia coliO157:H7 strain. In still other embodiments, a glutamate decarboxylase ofthe invention is from a Shigella species. In some embodiments, twoglutamate decarboxylases may be present in the same strain (GadA andGadB). In some embodiments, the clcA gene from E. coli is present in thechromosome and transcribed from its own native promoter, a heterologousconstitutive promoter or a heterologous regulatable promoter.

In a different embodiment, a recombinant bacterium of the inventioncomprises a mutation in at least one of aroD, guaBA, rpoS, fur, orphoPQ. In some embodiments, the regulatable acid resistance cassette isregulated by a sugar-inducible promoter. The recombinant bacterium isacid sensitive in the absence of inducer for the regulateable acidresistance cassette. In particular embodiments, the promoter isresponsive to the presence of rhamnose or arabinose. In some exemplaryembodiments, the acid resistance mechanism is composed of a ureaseenzyme. In further embodiments, accessory proteins such as aproton-gated urea channel, carbonic anhydrase or enzyme chaperones willcomprise additional components of the acid resistance mechanism. Inparticular embodiments, the urease, urease channel, carbonic anhydraseand apoenzyme chaperones are derived from a Helicobacter species. Inother specific embodiments, the components that comprise the acidresistance mechanism are UreA, UreB, UreI, UreE, UreF, UreG, UreH andHP1186 from Helicobacter pylori.

In several exemplary embodiments, a recombinant bacterium of theinvention is acid sensitive, is a Salmonella Typhi bacterium adapted foruse as a live attenuated vaccine, and the arginine decarboxylase and thearginine agmatine antiporter comprising the regulatable cassette areadiA and adiC from Salmonella Typhi.

In one exemplary embodiment, a recombinant bacterium of the inventioncomprises a mutation in at least one of aroD, guaBA, rpoS, fur, or phoPQthat renders the bacterium acid sensitive in the absence of rhamnose,and comprises a ΔP_(adiA)::TT rhaSR P_(rhaBAD) adiAC mutation.

In another exemplary embodiment, a recombinant bacterium of theinvention comprises a mutation in at least one of aroD, guaBA, rpoS,fur, or phoPQ that renders the bacterium acid sensitive in the absenceof arabinose, and comprises a ΔP_(adiA)::TT araC P_(araBAD) adiACmutation.

In several exemplary embodiments, a recombinant bacterium of theinvention is acid sensitive, is a Salmonella Typhi bacterium adapted foruse as a live attenuated vaccine, and the glutamate decarboxylase and aglutamate/γ-aminobutyric acid antiporter comprising the regulatablecassette are gadB and gadC from Escherichia coli.

In one exemplary embodiment, a recombinant bacterium of the inventioncomprises a mutation in at least one of aroD, guaBA, rpoS, fur, or phoPQthat renders the bacterium acid sensitive in the absence of rhamnose,and comprises a ΔP_(gadB):: TT rhaSR P_(rhaBAD) gadBC mutation.

In another exemplary embodiment, a recombinant bacterium of theinvention is a S. Typhi strain comprising a mutation in at least one ofaroD, guaBA, rpoS, fur, or phoPQ that renders the bacterium acidsensitive in the absence of arabinose, and comprises a ΔcysG::TT araCP_(BAD) gadBC mutation.

In still another exemplary embodiment, a recombinant bacterium of theinvention comprises a mutation in at least one of aroD, guaBA, rpoS,fur, or phoPQ that renders the bacterium acid sensitive in the absenceof arabinose, and comprises a AP_(gadB)::TT araC P_(BAD) gadBC mutation.

In several exemplary embodiments, a recombinant bacterium of theinvention is acid sensitive, is a Salmonella Typhi bacterium adapted foruse as a live attenuated vaccine, and the lysine decarboxylase and alysine/cadaverine antiporter comprising the regulatable cassette arecadB and cadA from Salmonella Typhi.

In one exemplary embodiment, a recombinant bacterium of the inventioncomprises a mutation in at least one of aroD, guaBA, rpoS, fur, or phoPQthat renders the bacterium acid sensitive in the absence of rhamnose,and comprises a ΔP_(cadB):: TT rhaSR P_(rhaBAD) cadBA mutation.

In another exemplary embodiment, a recombinant bacterium of theinvention comprises a mutation in at least one of aroD, guaBA, rpoS,fur, or phoPQ that renders the bacterium acid sensitive in the absenceof arabinose, and comprises a ΔP_(cadB)::TT araC P_(BAD) cadBA mutation.

In still another exemplary embodiment, a recombination bacterium of theinvention is a Salmonella enterica serovar Gallinarum (S. Gallinarum)comprising a mutation in at least one of pmi or fur that renders thebacterium sensitive in the absence of arabinose, and comprises aΔcysG::TT araC P_(BAD) gadBC mutation.

In other exemplary embodiments, a recombinant bacterium of the inventionis a Salmonella enterica serovar Dublin (S. Dublin) comprising aΔP_(adiA)::TT rhaSR R_(rhaBAD) adiA Δ(P_(adiY)::-adiY-P_(adiC)) adiCmutation or a ΔcysG::TT araC P_(BAD) gadBC mutation.

II. Vaccine Compositions and Administration

A recombinant bacterium of the invention may be administered to a hostas a vaccine composition. As used herein, a vaccine composition is acomposition designed to elicit an immune response to the recombinantbacterium, including any antigens that may be expressed by thebacterium. In an exemplary embodiment, the immune response isprotective, as described above. Immune responses to antigens are wellstudied and widely reported. A survey of immunology is given by Paul, WE, Stites D et.al. and Ogra P L. et.al. Mucosal immunity is alsodescribed by Ogra P L et.al.

Vaccine compositions of the present invention may be administered to anyhost capable of mounting an immune response. Such hosts may include allvertebrates, for example, mammals, including domestic animals,agricultural animals, laboratory animals, and humans, and variousspecies of birds, including domestic birds and birds of agriculturalimportance. Preferably, the host is a warm-blooded animal. The vaccinecan be administered as a prophylactic or for treatment purposes.

In exemplary embodiments, the recombinant bacterium is alive whenadministered to a host in a vaccine composition of the invention. Infurther exemplary embodiments, a recombinant bacterium comprising avaccine of the invention is derived from Salmonella Typhi. In stillfurther exemplary embodiments, a recombinant bacterium comprising avaccine of the invention is derived from Salmonella Typhi Ty2. Suitablevaccine composition formulations and methods of administration aredetailed below.

(a) Vaccine Composition

A vaccine composition comprising a recombinant bacterium of theinvention may optionally comprise one or more possible additives, suchas carriers, preservatives, stabilizers, adjuvants, and othersubstances.

In one embodiment, the vaccine comprises an adjuvant. Adjuvants, such asaluminum hydroxide or aluminum phosphate, are optionally added toincrease the ability of the vaccine to trigger, enhance, or prolong animmune response. In exemplary embodiments, the use of a live attenuatedrecombinant bacterium may act as a natural adjuvant. The vaccinecompositions may further comprise additional components known in the artto improve the immune response to a vaccine, such as T cellco-stimulatory molecules or antibodies, such as anti-CTLA4. Additionalmaterials, such as cytokines, chemokines, and bacterial nucleic acidsequences naturally found in bacteria, like CpG, are also potentialvaccine adjuvants.

In another embodiment, the vaccine may comprise a pharmaceutical carrier(or excipient) used to resuspend the lyophilized RASV. Live RASVs aregenerally lyophilized in the presence of various types of protectants,very often sugars, than enhance thermal stability and are reconstitutedat time of use. Such a carrier may be any solvent or solid material forencapsulation that is non-toxic to the inoculated host and compatiblewith the recombinant bacterium. A carrier may give form or consistency,or act as a diluent. Suitable pharmaceutical carriers may include liquidcarriers, such as normal saline and other non-toxic salts at or nearphysiological concentrations, and solid carriers not used for humans,such as talc or sucrose, or animal feed. Carriers may also includestabilizing agents, wetting and emulsifying agents, salts for varyingosmolarity, encapsulating agents, buffers, and skin penetrationenhancers. Carriers and excipients as well as formulations forparenteral and nonparenteral drug delivery are set forth in Remington'sPharmaceutical Sciences 19th Ed. Mack Publishing (1995). When used foradministering via the bronchial tubes, the vaccine is preferablypresented in the form of an aerosol.

Care should be taken when using additives so that the live recombinantbacterium is not killed, or have its ability to effectively colonizelymphoid tissues such as the GALT, NALT and BALT compromised by the useof additives. Stabilizers, such as lactose or monosodium glutamate(MSG), may be added to stabilize the vaccine formulation against avariety of conditions, such as temperature variations or a freeze-dryingprocess.

The dosages of a vaccine composition of the invention can and will varydepending on the recombinant bacterium, the regulated antigen, and theintended host, as will be appreciated by one of skill in the art.Generally speaking, the dosage need only be sufficient to elicit aprotective immune response in a majority of hosts. Routineexperimentation may readily establish the required dosage. Typicalinitial dosages of vaccine for oral administration could be about 1×10⁷to 1×10¹⁰ CFU depending upon the age of the host to be immunized.Administering multiple dosages may also be used as needed to provide thedesired level of protective immunity.

In an embodiment, a vaccine composition of the invention may beadministered in combination with a compound to reduce the pH of thegastric components. The compound may be used to buffer the stomach pH ofa subject. Buffering the pH of the stomach may further enhance theimmune response elicited in response to a vaccine composition. In anexemplary embodiment, Ensure® may be administered in combination with avaccine composition. In another exemplary embodiment, sodium bicarbonatemay be administered in combination with a vaccine composition.

(b) Methods of Administration

In order to stimulate a preferred response of the GALT, NALT or BALTcells, administration of the vaccine composition directly into the gut,nasopharynx, or bronchus is preferred, such as by oral administration,intranasal administration, gastric intubation or in the form ofaerosols, although other methods of administering the recombinantbacterium, such as intravenous, intramuscular, subcutaneous injection orintramammary, intrapenial, intrarectal, vaginal administration, or otherparenteral routes, are possible.

In some embodiments, these compositions are formulated foradministration by injection (e.g., intraperitoneally, intravenously,subcutaneously, intramuscularly, etc.). Accordingly, these compositionsare preferably combined with pharmaceutically acceptable vehicles suchas saline, Ringer's solution, dextrose solution, and the like.

III. Kits

The invention also encompasses kits comprising any one of thecompositions above in a suitable aliquot for vaccinating a host in needthereof. In one embodiment, the kit further comprises instructions foruse. In other embodiments, the composition is lyophilized such thataddition of a hydrating agent (e.g., buffered saline) reconstitutes thecomposition to generate a vaccine composition ready to administer,preferably orally.

IV. Methods of Use

A further aspect of the invention encompasses methods of using arecombinant bacterium of the invention. For instance, in one embodimentthe invention provides a method for modulating a host's immune system.The method comprises administering to the host an effective amount of acomposition comprising a recombinant bacterium of the invention. One ofskill in the art will appreciate that an effective amount of acomposition is an amount that will generate the desired immune response(e.g., mucosal, humoral or cellular). Methods of monitoring a host'simmune response are well-known to physicians and other skilledpractitioners. For instance, assays such as ELISA, and ELISPOT may beused. Effectiveness may be determined by monitoring the amount of theantigen of interest remaining in the host, or by measuring a decrease indisease incidence caused by a given pathogen in a host. For certainpathogens, cultures or swabs taken as biological samples from a host maybe used to monitor the existence or amount of pathogen in theindividual.

In another embodiment, the invention provides a method for eliciting animmune response against an antigen in a host. The method comprisesadministering to the host an effective amount of a compositioncomprising a recombinant bacterium of the invention.

In still another embodiment, a recombinant bacterium of the inventionmay be used in a method for eliciting an immune response against apathogen in an individual in need thereof. The method comprisesadministrating to the host an effective amount of a compositioncomprising a recombinant bacterium as described herein. In a furtherembodiment, a recombinant bacterium described herein may be used in amethod for ameliorating one or more symptoms of an infectious disease ina host in need thereof. The method comprises administering an effectiveamount of a composition comprising a recombinant bacterium as describedherein.

In a further embodiment, the present invention encompasses a method forincreasing the acid resistance of an acid sensitive bacterium. Themethod comprises introducing into the acid sensitive bacterium acassette comprising a regulatable promoter operable linked to anarginine decarboxylase and an arginine agmatine antiporter as describedin Section I above. Alternatively, the method comprises introducing intothe acid sensitive bacterium a cassette comprising a regulatablepromoter operable linked to a glutamate decarboxylase and aglutamate/γ-aminobutyric acid antiporter as described in Section Iabove. In another embodiment, the method comprises introducing into theacid sensitive bacterium a cassette comprising a regulatable promoteroperable linked to a lysine decarboxylase and a lysine/cadaverineantiporter as described in Section I above. Upon induction of theregulatable promoter, the recombinant bacterium experiences an increasein acid resistance. In some variations of these embodiments, theregulatable promoter may be induced by a sugar, such as rhamnose orarabinose. In other variations of these embodiments, the recombinantbacterium comprises a mutation in at least one nucleic acid sequenceselected from the group consisting of aroD, guaBA, rpoS, fur, and phoPQ.

In yet still another embodiment, the present invention encompasses amethod of increasing the survival of probiotic bacteria during passagethrought the stomach. The method comprises introducing into theprobiotic bacterium a cassette comprising a regulatable promoteroperable linked to an arginine decarboxylase and an arginine agmatineantiporter as described in Section I above. Alternatively, the methodcomprises introducing into the probiotic bacterium a cassette comprisinga regulatable promoter operable linked to a glutamate decarboxylase anda glutamate/γ-aminobutyric acid antiporter as described in Section Iabove. In another embodiment, the method comprises introducing into theprobiotic bacterium a cassette comprising a regulatable promoteroperable linked to a lysine decarboxylase and a lysine/cadaverineantiporter as described in Section I above. Upon induction of theregulatable promoter, the recombinant bacterium experiences an increasein acid resistance. In some variations of these embodiments, theregulatable promoter may be induced by a sugar, such as rhamnose orarabinose. According to this method, the probiotic bacterium survivesthe low pH stomach environment and effectively colonizes the subject.

The following examples are included to demonstrate preferred embodimentsof the invention. It should be appreciated by those of skill in the artthat the techniques disclosed in the examples that follow representtechniques discovered by the inventors to function well in the practiceof the invention. Those of skill in the art should, however, in light ofthe present disclosure, appreciate that may changes can be made in thespecific embodiments that are disclosed and still obtain a like orsimilar result without departing from the spirit and scope of theinvention, therefore all matter set forth or shown in the accompanyingdrawings is to be interpreted as illustrative and not in a limitingsense.

EXAMPLES

The following examples are simply intended to further illustrate andexplain the present invention. The invention, therefore, should not belimited to any of the details in these examples.

Introduction

Before orally ingested enteric pathogens such as Salmonella can reachtheir target host cells, they must first survive their encounter withthe low pH of the human stomach; approximately 2.0 following a fast (1).This is an extremely hostile environment for wild-type Salmonella, thusSalmonella contains multiple regulatable systems to aid in survival atlow pH (2, 3). The best studied of these systems is the acid toleranceresponse (ATR). Cells exposed to moderately low pH synthesize numerousacid shock proteins. Although the specific functions of these proteinsare largely unknown, jointly they mitigate the proton damage experiencedby the cell during low pH challenge (pH 3.0) (4, 5). The acid toleranceresponse is a complex multi-component system coordinated by a number ofglobal regulatory proteins. In stationary phase, RpoS is a key regulatorof the acid tolerance response. Not only does the acid toleranceresponse of an rpoS mutant fail to provide the same level of protectionas in a wild-type strain, but rpoS mutants are unable to sustain theacid tolerance response, resulting in rapid cell death upon pH 3.0challenge (4, 6). In log phase cells, the Salmonella virulence proteinsPhoP/PhoQ and Fur regulate the acid tolerance response. Fur controls asubset of acid shock proteins essential for protecting the cell againstorganic acid challenge while PhoP/PhoQ coordinates protection againstinorganic acid challenge (7, 8).

The vast majority of live attenuated Salmonella vaccines for humans areconstructed from Salmonella Typhi strain Ty2, an rpoS mutant (9). Tocreate a vaccine, additional attenuating mutations are necessary invirulence genes. However, these mutations can affect more than justvirulence. In addition to the rpoS mutation derived from its parentstrain Ty2, the licensed typhoid vaccine strain Ty21a carries galE andtvi mutations as well as a number of other, less well-characterized,mutations (10-12). The strain is sensitive to low pH, due at least inpart to its inability to mount a functional acid tolerance response(13). Another vaccine strain, Ty800, contains a deletion of the phoPQlocus. This strain is safe and reasonably immunogenic in humans (14),but one would expect that the combination of the phoPQ deletion and rpoSmutation would render this strain exquisitely sensitive to acidic pH (6,8). A similar situation occurs for the vaccine strains χ9639(pYA4088)and χ9640(pYA4088) (15). These strains are also safe and immunogenic inhumans (69), but the mutation in their fur locus leaves them vulnerableto low pH.

Most vaccine researchers avoid the problem low gastric pH poses bycoating their vaccine in a protective enteric capsule (e.g. Ty21a) or byco-administering an antacid (usually sodium bicarbonate) at the time ofimmunization (16-21). Preventing vaccine exposure to low pH increasesthe number of viable cells that reach the intestine and improves vaccineimmunogenicity (21, 22).The disadvantage of bypassing the acidicenvironment of the stomach is that the low pH encounter serves as animportant signal to Salmonella, allowing it to recognize entry into ahost environment. Exposure to acid stimulates up-regulation of the genesthat confer resistance to the short chain fatty acids (23),antimicrobial peptides (24) and osmotic stress (6) found in theintestine. Also, induction of the acid tolerance response has beenlinked to upregulation of SPI-1 and SPI-2 and an increase in epithelialcell invasion in the intestine (25-27). Thus, transient exposure to lowpH prepares the invading bacteria for the stresses of the intestine andfor host-cell interactions. Therefore, it is possible that if we canenhance the survival rate of live attenuated Salmonella vaccine strainsat low pH, we can not only eliminate the need for low pH bypassstrategies but also improve the ability of the vaccine strain tointeract with host tissues to enhance immunogenicity.

As a first step toward this goal, we explored methods to increase thelow pH survival of S. Typhi strains containing rpoS, phoPQ or furmutations, because each renders strains acid sensitive and each has beenincorporated into live attenuated vaccine strains. One robust means usedby Salmonella to resist low pH challenge is the arginine decarboxylaseacid resistance system (AR3) (28). This system consists of argininedecarboxylase (AdiA) and an arginine-agmatine antiporter (AdiC) (29).Acid resistance is conferred by the activity of AdiA, which consumes oneproton from the intracellular environment with each reaction cycle andcauses a rapid rise in intracellular pH (30, 31). AdiC then exchangesthe agmatine reaction product to the periplasm in exchange for anotherarginine substrate molecule(29, 32).The combined activities of AdiA andAdiC allow Salmonella to resist pH 2.5 for greater than two hours(3).

Because the arginine decarboxylase system functions independently of theacid tolerance response, we hypothesized that synthesis of AdiA and AdiCwould confer high levels of acid resistance on strains containingmutations that affect acid tolerance such as rpoS, phoPQ and fur.However, the arginine decarboxylase system is tightly regulated and isnot normally available to cells grown under standard vaccine cultureconditions (33). Therefore, we replaced the native promoter of argininedecarboxylase with the araBAD or rhaBAD promoter and compared the levelof arginine decarboxylase activity when cells were cultured in thepresence of arabinose and rhamnose, respectively. Once we selected thepromoter with optimal sugar-dependent expression and activity of thearginine decarboxylase system (P_(rhaBAD)), our objectives weretwo-fold. First, we determined if the rhamnose-regulated argininedecarboxylase system could rescue rpoS, phoPQ and fur mutants during lowpH challenge if cells were cultured in the presence of rhamnose butwithout any other environmental signals that would induce eitherdecarboxylase activity or the acid tolerance response. Second, todetermine whether the rhamnose-regulated system functioned equivalentlyto the native arginine decarboxylase system, we compared the level ofacid resistance afforded by the rhamnose-dependent argininedecarboxylase system with the acid resistance of rpoS, phoPQ and furmutants cultured under decarboxylase- and acid tolerance-inducingconditions.

Materials and Methods

DNA manipulation and plasmid construction. Chromosomal DNA from S. TyphiTy2 was isolated using the Wizard Genomic DNA Purification kit (Promega,Madison, Wis., USA). Plasmid DNA was isolated using QIAprep SpinMiniprep kit (QIAGEN, Valencia, Calif., USA) or the Wizard Plus MidiprepDNA Purification system (Promega). DNA inserts were amplified by PCRusing the Phusion DNA polymerase (New England Biolabs, lspwich, Mass.,USA) or the Easy-A high-fidelity PCR cloning enzyme (Agilent, SantaClara, Calif., USA). Restriction and modification enzymes for cloning(New England Biolabs) were used in accordance with the manufacturer'sinstructions.

Construction of S. Typhi mutants. The bacterial strains and plasmidsused in this study are listed in Table 1. Primers used during theconstruction of plasmids are listed in Table 2. To construct the ΔaroDmutation, two DNA fragments adjacent to the aroD gene were amplifiedfrom the chromosome of Ty2. Primers Aro-1 and -2 were used for theupstream fragment, while primers Aro-3 and -4 were used for thedownstream fragment. These fragments were digested with BamHl, ligatedusing T4 DNA ligase, re-amplified by PCR with primers Aro-1 and -4 andcloned into the Ahdl sites of pYA4278 via TA overhangs to generate thesuicide vector pYA4895. The ΔaroD deletion was introduced into Ty2 byconjugation as described by Kaniga (34). The resulting strain (χ11548)exhibits aromatic amino acid auxotrophy and carries a deletion of thecomplete coding sequence of aroD that spans 759 bp.

An arabinose-regulated fur mutant was constructed via P22 HT inttransduction (35) using a lysate grown on χ9269 containing achromosomally integrated copy of pYA4181 (36) to create the S. Typhistrain χ11118. The presence of the ΔP_(fur)::TT araC P_(BAD) furmutation in S. Typhi was confirmed by PCR using the primers Fur-1 and-2. Arabinose-dependent synthesis of Fur was verified by western blot.

To remove the entire adi locus (A(adiA-adiC)), the upstream anddownstream flanking regions in Ty2 were amplified using PCR primersAdi-1 and -2 and primers Adi-3 and -4, respectively. The flankingregions were digested with BamHl and ligated together with T4 DNAligase. The resulting product was re-amplified by PCR using primersAdi-1 and -4 and cloned into the Ahdl sites of pYA4278 to generate thesuicide vector pYA5066. The A(adiA-adiC) mutation (hereafter(ΔadiA-adiC) encoded by pYA5066 was moved into Ty2 to create χ11500.This strain carries a 4806-bp deletion of the adi locus (complete codingsequences of adiA, adiY and adiC along with the adiY and adiC promoters)(FIG. 1). The absence of the adi locus was confirmed by PCR and byarginine decarboxylase assay.

Two mutations were constructed that placed adiA under the control ofsugar-responsive promoters—A66 P_(adiA)::TT araC P_(araBAD) adiA(regulated by arabinose) and ΔP_(adiA)::TT rhaSR P_(rhaBAD) adiA(regulated by rhamnose). For simplicity, these mutations will bereferred to as P_(araBAD) adiA and P_(rhaBAD) adiA, respectively. Forthe arabinose-regulated construct, the DNA regions flanking the adiApromoter were amplified by PCR from Ty2 using primers Adi-5 and-6 forthe upstream region and primers Adi-7 and -8 for the downstream region.Both flanking regions were cloned into pYA3700 (using SphI and BgIII forthe upstream region and KpnI and SacI for the downstream region) togenerate pYA5075. The DNA segment containing the flanking regions andarabinose promoter was amplified by PCR using Adi-5 and -8 and the PCRproduct was cloned into the Ahdl sites of pYA4278 to create the suicidevector pYA5089. To generate the rhamnose-regulated construct, the araCP_(araBAD) promoter of pYA5089 was removed by XhoI and XbaI doubledigestion. The rhaSR P_(rhaBAD) promoter from pYA5081 was amplified byPCR with the Rha-1 and -2 primers and cloned into pYA5089 using XhoI andXbaI to produce the suicide vector pYA5093. pYA5089 and pYA5093 wereintroduced into χ11548 by conjugation to produce χ11552 and χ11564,respectively. The juxtaposition of adiA with the appropriate promoterwas verified by PCR with the Ara-1 and Adi-9 primers (χ11552) or Rha-3and Adi-9 primers (χ11564) and by arginine decarboxylase assay. In bothstrains, 203 bp of the intergenic region between melR and adiA(including the -10 and -35 sites of the adiA promoter) were deleted andreplaced with either TT araC P_(araBAD (χ)11552) or TT rhaRSP_(rhaBAD (χ)11564). The strong transcription terminator T4 ip III wasplaced between the upstream melR gene and araC or rhaSR to preventexpression of anti-sense RNA. A strong Shine-Dalgarno site (AGGA) wasinserted 10 bp upstream of the ATG start codon of adiA (FIG. 1).

The adiC gene was fused into an operon with adiA resulting in theΔ(P_(adiY)-adiY-P_(adiC)) adiC mutation (hereafter adiAC). The DNAregions flanking adiY were amplified by PCR from Ty2 using primersAdi-10 and -11 for the upstream region and primers Adi-12 and -13 forthe downstream region. The two DNA segments were joined by overlap PCRand re-amplification with Adi-10 and -13. The final PCR product wasligated into pYA4278 at the Ahdl sites to produce the suicide vectorpYA5072. The suicide vector was introduced into χ11564 and χ11548 byconjugation to produce χ11568 (ΔaroD P_(rhaBAD) adiAC) and χ11636 (ΔaroDadiAC), respectively. The presence of the adiAC operon was confirmed byPCR using Adi-14 and -15. Both strains harbor a 1078-bp deletion thatspans the transcription terminator following adiA, adiY and the promoterof adiC. The adiA and adiC genes are separated by a 119-bp intergenicsequence expected to decrease expression of adiC from the promoterupstream of adiA (FIG. 1).

Growth conditions and culture media. Experiments testing the regulationof arabinose- and rhamnose-controlled genes were conducted in thecarbohydrate-free medium purple broth (BD Biosciences, Franklin Lakes,N.J., USA). For acid resistance experiments, strains were propagated intryptic soy broth (TSB) (BD Biosciences) with 0.4% glucose, or inminimal E medium, pH 7.0 with 0.4% glucose (EG medium) (37). For ourexperiments, 22 μg/ml L-cysteine, 20 μg/ml L-tryptophan and 0.1%casamino acids were added to EG medium in order to supplement the growthof all strains (EGA medium). For strains with the ΔaroD mutation, 20μg/ml L-tryptophan, 2 μg/ml p-aminobenzoic acid and 2.5 μg/ml 2,3-dihydroxybenzoate were added to all media. EGA medium was additionallysupplemented with 50 μg/ml L-phenylalanine and 20 μg/ml L-tyrosine.Rhamnose was added to 0.1% or to 0.4% in the case of strain χ11623, asindicated. Strains containing the ΔP_(fur)::TT araC P_(araBAD) furmutation were supplied with 0.2% arabinose unless otherwise indicated.All chemicals were purchased from Sigma-Aldrich (St. Louis, Mo., USA) orThermo Fisher Scientific (Pittsburgh, Pa., USA) unless otherwiseindicated.

Measurement of adiA expression by semi-quantitative PCR. Strains weregrown in purple broth with varying concentrations of rhamnose orarabinose to an optical density at 600 nm (OD₆₀₀) of 0.6. Total cellularRNA was isolated using the RNeasy Mini Kit (QIAGEN) and was treated withRNase-free DNase (QIAGEN). cDNA was generated via reversetranscription-PCR (RT-PCR) using 1 μg of cellular RNA with the TaqManReverse Transcriptase kit (Life Technologies, Grand Island, N.Y.) underthe following conditions: 10 minutes at 25° C. for optimal randomhexamer primer binding, then 45 minutes at 48° C. for extension followedby 5 minutes at 95° C. to heat inactivate the transcriptase.Semi-quantitative PCR of the adiA and gapA transcripts was performedusing the GoTaq DNA Polymerase system (Promega) using primers SQ-1 andSQ-2 for gapA and SQ-3 and SQ-4 for adiA under the following conditions:2.5 minutes at 95° C. for template denaturation, followed by 28 cyclesof 40s at 95° C., 30 s at 48° C. for primer annealing and 1 minute at72° C. for primer extension. The semi-quantitative PCR primer sequencesare listed in Table 2 (SQ1-SQ4). PCR products were electrophoresed on a2% agarose gel in the presence of ethidium bromide and visualized withthe Chemi Doc XRS System (Bio-Rad Laboratories, Hercules, Calif., USA).Images were analyzed in Adobe PhotoshopCS4 (Adobe Systems Incorporated,San Jose, Calif., USA) in order to establish histogram values for thefluorescence signal intensity of the PCR products. Signal intensityvalues for adiA were normalized to the value obtained with the singlegene expression control gapA for each culture.

Preparation of antiserum against arginine decarboxylase protein. E. coliBL21(DE3) harboring pYA5085 was used for the synthesis of His-taggedAdiA protein. Cells were grown in LB at 37° C. to mid-log phase (anoptical density value at 600 nm [OD₆₀₀] of 0.6). The growth medium wassupplemented with 0.2 g/L pyridoxine to augment protein folding andenzyme activity (38). Protein synthesis was induced with 1 mM IPTG(isopropyl β-D-1-thiogalactopyranoside) (Amresco, Solon, Ohio, USA) for4 hours at 37° C. Cells were collected by centrifugation and disruptedusing lysozyme (3 mg/g cells) and deoxycholic acid (120 mg/g cells)(39). His-tagged AdiA protein from the soluble fraction was purifiedover TALON™ metal affinity resin (BD Biosciences) in accordance with themanufacturer's instructions except that 10% ethanol was added to theelution buffer. Purified protein was stored in 20 mM HEPES, 50 mM NaCl,pH 8.0 (30).

One juvenile New Zealand white rabbit (Charles River Laboratories,Wilmington, Mass., USA) was immunized with 200 μg of AdiA emulsified inFreund's complete adjuvant, and boosted with an additional 200 μg ofAdiA emulsified in Freund's incomplete adjuvant 4 weeks and 8 weeksafter the initial injection. Serum was collected 3 weeks following thefinal immunization.

Western blot procedure. Strains were grown overnight at 37° C. in purplebroth containing various concentrations of rhamnose or arabinose. Theamount of total cellular protein in each sample was normalized byabsorbance at 280 nm using the NanoDrop ND-1000 (Thermo Scientific,Wilmington, De., USA). Equal amounts of cellular protein (100 μg forAdiA; 150 μg for Fur) were mixed with 2× SDS-PAGE buffer, boiled, andelectrophoresed on a 10% acrylamide gel (40). Separated proteins weretransferred to a PVDF membrane (Bio-Rad) using Towbin's wet transfermethod (41), blocked in 5% skim milk, then probed with rabbit antiserum(final dilution 1:10,000) for the presence of AdiA or Fur (36). Boundprimary antibody was detected by the addition of goat anti-rabbit IgGconjugated to alkaline phosphatase (Sigma-Aldrich). Blots were developedwith NBT/BCIP (Amresco) and photographed using the ChemiDocXRS System.

Arginine decarboxylase assays. Arginine decarboxylase enzyme activitywas measured using a modified version of the rapid glutamatedecarboxylase assay previously described (42). Strains were grownovernight (18 h) to stationary phase in purple broth, washed once inphosphate buffered saline (PBS) (39)and normalized to an OD₆₀₀ value of0.7. Five ml of normalized cells were pelleted, resuspended in 2.5 mlarginine decarboxylase assay medium [1 g L-arginine, 0.05 g bromocresolgreen, 90 g NaCl, and 3 ml Triton X-100 per liter of distilled water(adjusted to pH 3.4)] and vortexed for 30 s. Assay tubes were incubatedat 37° C. for 5-30 minutes, scored and photographed.

Acid resistance assays. Acid resistance was determined essentially asdescribed previously (43, 44) with the following modifications. Strainswere grown overnight to stationary phase in minimal EGA medium at pH 7.0(37) or in TSB with 0.4% glucose. Cultures were normalized to the sameOD₆₀₀, then pelleted and washed once in EGA medium, pH 7.0 containing nogrowth supplements. Cells were pelleted a second time and resuspended ata density of 1×10⁹ CFU/ml in EGA medium containing 1 mM L-arginine at pH3.0, 2.5 or 2.0. Low pH challenge was conducted at 37° C. and sampleswere collected immediately after resuspension (t=0) and hourly for 4 h.Samples were serially diluted and plated onto LB agar to assessviability during challenge.

Statistical analyses. All statistical analyses were performed usingGraphPad Prism version 5.04 for Windows(GraphPad Software, San Diego,Calif. USA, www.graphpad.com). Survival curves for 4-hour acidresistance assays were compared using two-way repeated measures (mixedmodel) ANOVA with Bonferroni's post-test. Data from 1 h acid resistancechallenges were compared using the paired t test.

RESULTS Example 1 Comparison of adiA Regulation from Arabinose- andRhamnose-Regulated Promoters

Genes encoding the arginine decarboxylase system are normally expressedin Salmonella only under anaerobic conditions (3, 33). To allowexpression during aerobic growth, we constructed two conditional adiAmutants that resulted in strains in which adiA expression was regulatedby either the araBAD or rhaBAD promoter. For safety, the sugar-regulatedadiA constructions were introduced into S. Typhi strain χ11548, whichcarries an attenuating ΔaroD mutation (17, 45).Thus, in strains χ11552(ΔaroD P_(araBAD) adiA) and χ11564 (ΔaroD P_(rhaBAD) adiA), adiAexpression should be responsive to the levels of exogenous arabinose orrhamnose, respectively. In the absence of the regulating sugar, bothstrains expressed low levels of adiA transcript consistent withbackground levels observed in Ty2 cultured under non-inducing conditionsfor adiA (FIG. 2A). Both strains increased production of the adiA mRNAtranscript when 0.1% (10⁻¹%) of the appropriate sugar was added.However, at lower sugar concentrations, the two strains behaveddifferently. Strain χ11552 (P_(araBAD) adiA) continued to expresselevated amounts of adiA mRNA at arabinose concentrations as low as0.0015 (10⁻³%). Only when the arabinose concentration fell below 0.001%(10⁻³%) did the amount of adiA transcript return to background levels.In contrast, strain χ11564 (P_(rhaBAD) adiA) expressed adiA transcriptonly in the presence of 0.1% (10⁻¹%) rhamnose and produced backgroundlevels of adiA mRNA at lower rhamnose concentrations.

AdiA protein synthesis and enzyme activity levels presented a patternsimilar to the mRNA. χ11552 (P_(araBAD) adiA) synthesized AdiA over awide range of arabinose concentrations (10⁻¹-10⁻⁴% arabinose), while inχ11564 (P_(rhaBAD) adiA) AdiA was detected over a narrower range ofrhamnose concentrations (10⁻¹-10⁻²% rhamnose) (FIG. 2B). While thehighest amounts of AdiA in both strains were observed at the arabinoseand rhamnose concentrations that increased levels of adiA transcript,small amounts of AdiA were also detected at sugar concentrations thatdid not produce a measurable increase in the amount of adiA transcriptpresent (10⁻⁴% arabinose for χ11552 and 10⁻²% rhamnose for χ11564),which could reflect differences in the sensitivity of the two assays orto differences in the stability of the adiA mRNA transcript and AdiAprotein.

AdiA activity was evaluated by decarboxylase assay, in which activeenzyme raises the assay medium pH above 5.0, resulting in a color changefrom yellow-green (negative) to blue (positive). Arginine decarboxylaseactivity (FIG. 2C) correlated with detection of AdiA on the western blot(FIG. 2B) and could be detected in χ11552 (P_(araBAD) adiA) culturesgrown in the presence of arabinose concentrations as low as 10⁻³%. Anintermediate reaction suggestive of low levels of enzyme activity wasobserved at 10⁻⁴% arabinose. In contrast, arginine decarboxylaseactivity was observed in χ11564 (P_(rhaBAD) adiA) only at rhamnoseconcentrations greater than 10⁻²%. Because the rhamnose-regulatedP_(rhaBAD) promoter provided tighter control over AdiA synthesis andactivity than the arabinose-regulated P_(araBAD) promoter, we selectedthe ΔP_(adiA):TT rhaSR P_(rhaBAD) adiA mutation for further studies.

Example 2 Co-Regulation of adiA and adiC is Necessary for SurvivalDuring pH 3.0 Challenge

Our goal in introducing the P_(rhaBAD) adiA construct into S. Typhi wasto provide arginine-dependent acid resistance when cells were grownunder conditions when this system is not normally induced (non-inducingconditions). To test this, we performed low pH challenges on cells grownaerobically in minimal EGA medium.

However, while χ11564 (ΔaroD P_(rhaBAD) adiA) exhibitedrhamnose-regulatable arginine decarboxylase activity under theseconditions (data not shown), the survival profile of χ11564 (ΔaroDP_(rhaBAD) adiA) at pH 3.0 did not differ from that of Ty2 or its parentstrain χ11548 (ΔaroD) (FIG. 3). This is likely due to the fact thatarginine-dependent acid resistance requires substrate::product exchangeby AdiC in addition to proton consumption by AdiA (29). Based on this,we reasoned that the P_(rhaBAD) promoter in strain χ11564 (ΔaroDP_(rhaBAD) adiA) does not drive adiC expression due to the presence of atranscriptional terminator downstream of adiA and the intervening adiYgene. Thus, it is likely that adiC expression remains under the controlof its native promoter and is not induced by rhamnose (FIG. 1). Toco-regulate expression of both adiA and adiC, the intergenic regionbetween the two genes, including the regulatory gene adiYand the adiCpromoter, was deleted, resulting in the fusion of adiA and adiC into asingle operon under the control of the native adiA promoter, resultingin strain χ11636 (adiAC) (FIG. 1). The sensitivity of χ11636 to pH 3.0challenge was not significantly different from Ty2 and χ11548(ΔaroD)(p=0.327) (FIG. 3). The adiAC operon fusion was then placed undertranscriptional control of P_(rhaBAD) adiA resulting in strain χ11568(ΔaroD P_(rhaBAD) adiAC). When grown with 0.1% rhamnose, strain χ11568was highly resistant to pH 3.0 challenge (FIG. 3), displaying a 1,000to10,000-fold increase over Ty2 in the number of viable cells present atall time points during challenge (p<0.0001).

Example 3 Survival of Strain χ11568 During pH 3 Challenge is Rhamnose-and Arginine-Dependent

A number of acid resistance and acid tolerance mechanisms have beendescribed in stationary phase Salmonella. To confirm that theacid-resistant phenotype of χ11568 (ΔaroD P_(rhaBAD) adiAC) wasattributable to the rhamnose-regulated arginine decarboxylase system thestrain was tested for survival at pH 3.0 in the absence of rhamnose andarginine. When cultured in minimal EGA medium without rhamnose, χ11568(ΔaroD P_(rhaBAD) adiAC) displayed a survival profile indistinguishablefrom the wild-type Ty2 and parent strain χ11548 (ΔaroD) during pH 3.0challenge (FIG. 4A). Adding rhamnose to the EGA culture medium restoredthe acid resistance of χ11568 (ΔaroD P_(rhaBAD) adiAC), resulting in a1,000- to 10,000-fold higher survival rate when rhamnose was provided(p=0.001).

The acid resistance of χ11568 (ΔaroD P_(rhaBAD) adiAC) also depended onthe presence of arginine in the challenge medium (FIG. 4B). Thepercentage of viable χ11568 (ΔaroD P_(rhaBAD) adiAC) cells duringchallenge rapidly declined over 4 hours in the absence of arginine, withfew survivors detected after the first two hours. However, cells thatwere challenged in the presence of 1 mM arginine showed a markedincrease in survival (p=0.003). Interestingly, removing arginine fromthe challenge medium also impaired survival of Ty2 (p=0.022), eventhough arginine decarboxylase activity was not detected under theseculture conditions (data not shown).

The rhamnose-regulated arginine decarboxylase system provided asubstantial benefit to S. Typhi survival during pH 2.5 challenge (FIG.5). After 1 hour at pH 2.5, χ11568 (ΔaroD P_(rhaBAD) adiAC) survived notonly significantly better than its ΔaroD parent (χ11548)(ΔaroD)(p=0.010), but also significantly better than the wild type(p=0.010) and arginine decarboxylase knockout χ11500 (p=0.035). Of the10⁹ CFU that were challenged, over 10⁵ CFU of χ11568(ΔaroD P_(rhaBAD)adiAC) remained viable after one hour. Despite this high level ofsurvival and although previous reports indicated that the argininedecarboxylase system could protect Salmonella Typhimurium for greaterthan two hours at pH 2.5 (3), we did not detect any S. Typhi survivorsafter the first hour of challenge (data not shown).

Example 4 Rescue of ΔphoPQ and ΔP_(fur)::TT araC P_(araBAD) fur Mutantsat pH 3 and 2.5

Because the rhamnose-regulated arginine decarboxylase system conferredsuch a high degree of acid resistance on χ11568(ΔaroD P_(rhaBAD) adiAC)when grown aerobically in minimal media (non-inducing conditions) (FIG.3), we tested the ability of this system to rescue two acid sensitivestrains of S. Typhi—a phoPQ mutant (χ8444) and a conditional fur mutant(χ11118). These mutations result in well-characterized acidsensitivities. Introducing the P_(rhaBAD) adiAC construct into strainsχ8444 (ΔphoPQ) and χ11118 (P_(araBAD) fur) resulted in strains χ11622and χ11623, respectively, that exhibited rhamnose-dependent argininedecarboxylase synthesis as described for χ11568 (ΔaroD P_(rhaBAD) adiAC)(FIG. 2C and data not shown).

To evaluate the ability of the rhamnose-regulated arginine decarboxylasesystem to rescue ΔphoPQ, strain χ11622 (ΔphoPQ P_(rhaBAD) adiAC) wasgrown in minimal EGA medium to stationary phase at pH 7.0 in thepresence of 0.1% rhamnose and then were challenged at either pH 3.0 orpH 2.5. Under these growth conditions, the ΔphoPQ mutant χ8444 displayeda similar survival profile as the wild-type Ty2 (p=0.996) (FIG. 6A). Incontrast, the survival of strainχ11622 (ΔphoPQ P_(rhaBAD) adiAC) wassignificantly greater than its parent strain χ8444 (ΔphoPQ) or thewild-type Ty2 (p=0.034). Further, strain χ11622 (ΔphoPQ P_(rhaBAD)adiAC) was significantly more resistant to a 1 h challenge at pH 2.5than any of the other S. Typhi strains (p=0.009 for χ8444; 0.010 for Ty2and 0.0232 for χ11500—ΔadiA-adiC) (FIG. 6B).

We next examined the impact of the arginine decarboxylase system on afur mutant (χ11623 (P_(araBAD) fur P_(rhaBAD) adiAC)). For thisanalysis, we utilized the conditional fur mutant χ11118 (P_(araBAD) fur)in which fur expression can be induced by addition of arabinose to theculture medium (36). However, western blot analysis indicated that,while Fur synthesis was induced by arabinose, the level of Fur producedin strain χ11118 (P_(araBAD) fur) was much less than the amount producedby Ty2 (FIG. 7A). Consistent with the low level of arabinose-induced Furproduction, the survival of pH 3.0-challenged cells grown in thepresence of 0.2% arabinose did not differ from that of cells grown inthe absence of arabinose (p=0.934) (FIG. 7B). Since χ11118 fur)(P_(araBAD) had the phenotype of a fur knockout in the acid resistanceassay irrespective of the arabinose concentration, we decided to workwith it and the rhamnose-regulated arginine decarboxylase daughterstrain (χ11623—P_(araBAD) fur P_(rhaBAD) adiAC) only in the absence ofarabinose. We observed no difference in survival at pH 3.0 between thewild-type Ty2, the arginine decarboxylase knockout χ11500 (ΔadiA-adiC)and χ11118 (P_(araBAD) fur) in our assay (p=0.392) (FIG. 7C). Strainχ11623 (P_(araBAD) fur P_(rhaBAD) adiAC) displayed greater survival thanits parent χ11118 (P_(araBAD) fur) for the first hour of challenge at pH3.0 (p=0.010) indicating that the arginine decarboxylase system couldrescue this fur mutant to some degree. However, there was no differencebetween χ11623 (P_(araBAD) fur P_(rhaBAD) adiAC)and χ11118 (P_(araBAD)fur) for the later time points (p=0.337). A similar trend was observedat pH 2.5 (FIG. 7D). χ11623 (P_(araBAD) fur P_(rhaBAD) adiAC) survivedsignificantly better after 1 hour at pH 2.5 than its acid-sensitiveparent χ11118 (P_(araBAD) fur) (p=0.013), but it was not significantlydifferent from the wild-type Ty2 (p=0.242) or the arginine decarboxylasemutant χ11500 (ΔadiA-adiC) (p=0.122).

Example 5 Rhamnose-Dependent Acid Resistance is Equivalent to AcidResistance in Cells grown Under Decarboxylase-Inducing Conditions

We next compared the level of acid resistance afforded by therhamnose-regulated system to the acid resistance provided by the nativesystem. Strains were grown anaerobically in unbuffered rich medium wherethe pH was allowed to fall below pH 5.0 during growth (native inducingconditions). Strains were supplied with 0.1% (or 0.4%, see below)rhamnose during growth. Cells were then challenged in EGA medium with 1mM arginine at pH 3.0 or 2.5. The arginine decarboxylase deletion mutantχ11500 (ΔadiA-adiC) rapidly succumbed to challenge at both pH 3.0 and2.5 (FIG. 8A, 8B). Ty2 and χ11548 (ΔaroD) displayed a high degree ofacid resistance at pH 3.0 (greater than 10⁴ CFU/ml were viable after 4hours), but succumbed to pH 2.5 after 2 hours. In contrast, the highlyacid resistant Shigella flexneri strain 2457T exhibited >70% viabilityfor 4 hours at pH 3.0 and viability only decreased by one log after 4hours at pH 2.5. Strain χ11568 (ΔaroD P_(rhaBAD) adiAC) was not able tomatch the acid resistance profile of Shigella, although it displayed asurvival profile equivalent to the S. Typhi Ty2 and χ11548(ΔaroD) grownunder these conditions (p=0.210). These results indicate that therhamnose-regulated system provides a level of acid resistance equivalentto the acid resistance afforded by the native system.

Under the native ad/A-inducing conditions, both phoPQ mutants, χ8444(ΔphoPQ) andχ11622 (ΔphoPQ P_(rhaBAD) adiAC), behaved similarly to Ty2during pH 3.0 challenge (p=0.498) (FIG. 8C). This was in contrast to thearginine decarboxylase deletion strain χ11500 (ΔadiA-adiC), whichsurvived significantly less well than the phoPQ strains at pH 3.0(p=0.018). No difference was observed in survival at pH 3.0 betweenχ8444 (ΔphoPQ) (which utilized the native arginine decarboxylase system)and χ11622 (ΔphoPQ P_(rhaBAD) adiAC) (which utilized therhamnose-regulated system) (p=0.628). A similar pattern was observed atpH 2.5 (FIG. 8D). No difference was observed between the native argininedecarboxylase system in χ8444 (ΔphoPQ) and the rhamnose-regulated systemin χ11622 (ΔphoPQ P_(rhaBAD) adiAC) (p=0.702).

Unlike χ11568 (ΔaroD P_(rhaBAD) adiAC) and χ11622 (ΔphoPQ P_(rhaBAD)adiAC), the conditional fur mutant χ11623(P_(araBAD) fur P_(rhaBAD)adiAC) did not produce detectable arginine decarboxylase activity in thepresence of 0.1% rhamnose when cultured in anaerobic rich medium.Arginine decarboxylase activity was detectable only when the rhamnoseconcentration was increased to 0.4% (data not shown). Therefore, theconcentration of rhamnose present in this assay was raised to 0.4% forχ11623(P_(araBAD) fur P_(rhaBAD) adiAC). In contrast to the phoPQmutants, the fur mutants χ11118 (P_(araBAD) fur) and χ11623 (P_(araBAD)fur P_(rhaBAD) adiAC) were significantly more sensitive to pH 3.0 thanthe wild-type Ty2 (FIG. 8E). χ11118 (P_(araBAD) fur) and χ11623(P_(araBAD) fur P_(rhaBAD) adiAC) displayed a survival profile moresimilar to that of χ11500 (ΔadiA-adiC) (p=0.392) than Ty2 (p=0.0006).However, there was no observable difference in survival between χ11118(P_(araBAD) fur) and χ11623 (P_(araBAD) fur P_(rhaBAD) adiAC) at eitherpH 3.0 (p=0.332) or pH2.5 (p=0.882) (FIG. 8F). These results indicatethat for both the ΔphoPQ and P_(araBAD) fur mutants, therhamnose-regulated arginine decarboxylase system and the native systemprovided equivalent levels of acid resistance.

Discussion of Examples 1 to 5

In this work, we constructed an acid resistance system whose expressionand activity responded to the presence of a single sugar, eitherarabinose or rhamnose. Both adiA and adiC expression were required foracid resistance (FIG. 3) and the rhamnose-regulated P_(rhaBAD) promoterprovided tighter control over adiA expression than thearabinose-regulated P_(araBAD) promoter (FIG. 2). The level of acidresistance provided by P_(rhaBAD) adiAC grown with rhamnose underdecarboxylase-inducing conditions was equivalent to the level of acidresistance observed with the native arginine decarboxylase system grownunder the same conditions. However, the rhamnose-regulated adiAC systemwas regulatable in cells otherwise unprepared for low pH challenge, thusour rhamnose-regulated system significantly improved the survival ofacid-unadapted aroD, phoPQ and fur mutants at pH 3 and 2.5 (FIGS. 3, 6and 7).

Comparison of the arabinose-regulated P_(araBAD) and rhamnose-regulatedP_(rhaBAD) promoters indicated that P_(rhaBAD) was less sensitive to itsregulatory sugar than P_(araBAD). At high concentrations of arabinose orrhamnose (0.1%), both promoters were active. The two promoters droveproduction of essentially equivalent amounts of adiA transcript at thisconcentration, consistent with previous results (46). As the amount ofregulatory sugar present in the culture was decreased, the activity ofthe two promoters decreased differentially. While background levels oftranscription were detected from P_(rhaBAD) at rhamnose concentrationsbelow 0.01% (10⁻²%), P_(araBAD) continued to function until thearabinose concentration fell below 0.0001° /o (10⁻⁴%). Some of thisdifference may be attributable to the “leakiness” of the P_(araBAD)promoter (47, 48). However, we used a modified sequence for P_(araBAD),which exhibits tightly controlled arabinose-dependent transcription(49).Since rhamnose is transported into Salmonella more efficiently thanarabinose, differences in sugar uptake are unlikely to be the cause ofthis discrepancy (50, 51). It is possible that rhamnose is converted toa non-inducing state following transport, because while neitherarabinose nor rhamnose can be fermented by S. Typhi (52), the rhaB andrhaA genes are intact and their gene products may be able to act on thetransported rhamnose. Another explanation is the previously observedslow rate of transcription from the P_(rhaBAD) promoter (53) resultingfrom the cascade of regulation by RhaR and RhaS on P_(rhaBAD) (51, 54)The reduced sensitivity of the P_(rhaBAD) promoter makes it an idealchoice to regulate the arginine decarboxylase system since it allowstight control of gene expression even in media containing trace amountsof rhamnose, such as LB and TSB.

Rhamnose-dependent acid resistance in S. Typhi depended on threethings—the presence of rhamnose in the culture medium, the presence ofarginine in the challenge medium, and the fusion of adiA and adiC intoan operon under the control of P_(rhaBAD). The absence of any of thesecomponents resulted in rapid cell death at pH 3.0 (FIGS. 3 and 4). Therequirement for co-regulation of adiA and adiC is consistent with theknown mechanism of the arginine decarboxylase system. Although AdiA isthe enzyme that consumes protons and is responsible for raising theintracellular pH during low pH challenge (55), AdiC is required toimport a continuous supply of arginine substrate from the periplasm(29). Deletions of either adiA or adiC abolish arginine-dependent acidresistance (3). The arginine requirement for survival at low pH confirmsthat the acid resistance we observed was due to the Salmonella argininedecarboxylase system and not to the stationary phase acid toleranceresponse or the oxidative acid resistance response (AR1), as neither ofthese systems requires arginine (2, 43). Interestingly, even thoughcells were cultured in aerobic minimal medium to prevent induction ofthe native arginine decarboxylase system in wild-type S. Typhi strainTy2 (3), we observed an arginine-dependent increase in resistance to pH3 challenge (FIG. 4B). This suggests that arginine decarboxylase isexpressed at low levels in S. Typhi during stationary phase culture—aconclusion consistent with the low, but detectable, levels of adiAtranscript observed in Ty2.

Substituting the rhamnose promoter P_(rhaBAD) for the native adiApromoter did not affect the degree of acid resistance afforded at lowpH. Strains with rhamnose-dependent acid resistance survived low pHchallenge as well as their respective parent strain cultured undernative decarboxylase-inducing conditions. Cells remained viable for over4 hours at pH 3.0 and for at least 2 hours at pH 2.5. No protection wasafforded against pH 2.0 challenge (data not shown), consistent withprevious reports for Salmonella (2, 56). By substituting the rhamnosepromoter for the native arginine decarboxylase promoter, we were able torescue χ11568 (ΔaroD P_(rhaBAD a)d/AC), a derivative of the rpoS mutantstrain Ty2, from low pH challenge via rhamnose induction of the argininedecarboxylase system (FIG. 3). χ11568 (ΔaroD P_(rhaBAD) adiAC) cellsgrown under non-inducing conditions (aerobic minimal medium, pH 7)remained viable for over 4 hours at pH 3 when rhamnose was included inthe growth medium. This indicates that the activity of the argininedecarboxylase system alone is sufficient for low pH survival in S.Typhi. However, χ11568 (ΔaroD P_(rhaBAD) adiAC) cultured underdecarboxylase-inducing conditions (anaerobic rich medium with 0.4%glucose) approximately 100-fold more cells survived pH 3 challenge thanwhen it was cultured aerobically in minimal medium (compare FIG. 3 andFIG. 7A). This is because the growth conditions necessary to inducearginine decarboxylase production in wild-type Salmonella simultaneouslyinduce the stationary phase acid tolerance response (3, 6, 57). Thedisparity in survival rates between cells cultured aerobically inminimal medium and cells cultured under fermentative conditionsunderscore the comprehensive nature of the acid response inSalmonella—maximum resistance to low pH is achieved by use of a varietyof strategies to counter the effects of low pH.

The rhamnose regulated arginine decarboxylase system was also able torescue a phoPQ mutant from low pH challenge (FIG. 6). Therhamnose-regulated arginine decarboxylase system in strain χ11622(ΔphoPQ P_(rhaBAD) adiAC) provided approximately a 1000-fold increase inviability at pH 3.0 over the parent phoPQ mutant (χ8444) when cells weregrown aerobically in minimal medium (cells unprepared for low pH). At pH2.5, the viability of χ11622 (ΔphoPQ P_(rhaBAD) adiAC) after 1 hourexceeded not only that of the parent phoPQ mutant, but also that of thewild-type Ty2. The success of our system at rescuing the phoPQ mutantmay be due to two reasons. First, the strains were challenged duringstationary phase, when PhoP/PhoQ are less important for acid tolerance(58). Second, a mutation in the phoPQ locus causes a very wellcharacterized sensitivity to inorganic acid (8). At low pH, inorganicacids exist almost exclusively in their dissociated state (free protonwith conjugate base), which makes them ideal candidates forneutralization by arginine decarboxylase (it will consume the freeprotons in the decarboxylase reaction, which immediately raises theintracellular pH and stops further cytoplasmic damage by the freeprotons). Thus the arginine decarboxylase system is well-poised tocompensate for the acid sensitivity imposed by a phoPQ mutation.

Survival of the P_(araBAD) fur mutant (χ11623) was enhanced byP_(rhaBAD) adiAC, although the improvement was not as great as it wasfor the ΔaroD and ΔphoPQ mutants. The addition of the rhamnose-regulatedarginine decarboxylase system improved viability during pH 3 and pH 2.5challenges, but unlike the phoPQ mutant, the fur mutant only benefittedduring the first hour of challenge (FIG. 7). The reason for thedifficulty of rescue may be two-fold. First, unlike phoPQ mutants, furmutants are sensitive to organic acids. Inorganic acids such as HCl andorganic acids behave quite differently inside the cell, due todifferences in their dissociation constants. Our EGA challenge mediumcontained not only the inorganic acid HCl, but also 10 mM citric acid(37). It is possible that the consumption of free protons by thearginine decarboxylase system is less effective at countering theeffects of an organic acid such as citric acid than the strong inorganicacid HCl (8, 23, 37, 59). Second, because the AP_(fur)::TT araCP_(araBAD) fur mutation was introduced into Ty2, the strain alsocontains an rpoS mutation. RpoS and Fur jointly regulate a number of keyeffectors responsible for protection against organic acid. Thus, thecombination of fur and rpoS mutations may have rendered χ11623 much moresensitive to acid than the rpoS mutation alone or the combination ofphoPQ and rpoS (4, 6). Finally, the P_(fur) mutation may have alteredthe ability of χ11623 to transport rhamnose, as it required four timesthe concentration of rhamnose to induce arginine decarboxylase activityas the aroD and phoPQ mutants. Fur is known to regulate expression of anumber of outer membrane proteins and other genes that may influencesurface structure (60). Thus, it is possible that membrane perturbationsdue to the lack of Fur in the cell may have resulted in a reduction inrhamnose transport activity by RhaT.

The construction of the rhamnose-regulated arginine decarboxylase systemallowed us to increase the acid resistance of S. Typhi (to pH 2.5) ondemand. Importantly, aerobically grown vaccine strains were protectedfrom pH 3 and pH 2.5. Since the low pH of the gastric environment posesa significant threat to the success of any live attenuated Salmonellavaccine, the rhamnose-regulated arginine decarboxylase system representsa novel means to augment survival in this in vivo compartment. Also,because low gastric pH is an important virulence signal, the ability toadminister vaccines without stomach pH neutralization may also improvevaccine performance in the host.

TABLE 1 Strains and plasmids used in this study Strain or Derivation orplasmid Genotype^(a) Source E. coli strains BL21 (DE3) F⁻ ompThsdS_(B)(r_(B) ⁻ m_(B) ⁻) gal dcm (DE3) Novagen χ7213 thr-1 leuB6 fhuA21lacY1 glnV44 recA1 ΔasdA4 Δ(zhf-2::Tn10) (61) thi-1 RP4-2-Tc::Mu [λpir]χ7573 Wild type O157:H7 strain 278F2 J. Giron S. Typhi strainsχ3769(Ty2) Wild-type, cys trp rpoS (62) χ8444 ΔphoPQ (63) χ11118ΔP_(fur)::TT araC P_(araBAD) fur Ty2 χ11500 Δ(adiA-adiC) Ty2 χ11548ΔaroD Ty2 χ11552 ΔaroD ΔP_(adiA)::TT araC P_(araBAD) adiA χ11548 χ11564ΔaroD ΔP_(adiA)::TT rhaSR P_(rhaBAD)adiA χ11548 χ11568 ΔaroDΔP_(adiA)::TT rhaSR P_(rhaBAD) adiA Δ(P_(adiY)-adiY-P_(adiC)) adiCχ11564 χ11622 ΔphoPQ ΔP_(adiA)::TT rhaSR P_(rhaBAD) adiAΔ(P_(adiY)-adiY-P_(adiC)) adiC χ8444 χ11623 ΔP_(fur)::TT araC P_(araBAD)fur ΔP_(adiA)::TT rhaSR P_(rhaBAD) adiA Δ(P_(adiY)-adiY- χ11118P_(adiC)) adiC χ11636 ΔaroD Δ(P_(adiY)-adiY-P_(adiC)) adiC χ11548 χ11742Δfur Ty2 Shigella flexneri strains 2457T S. flexneri 2a, wild-type, Pcr⁺Mal⁻ λ^(r) (64) Plasmids pET28a Protein synthesis vector, T7 promoter;Kan^(r) Novagen pJET1.2 Commercial cloning vector, pMB1 ori, Ap^(r)Thermo Scientific pUC18 Commercial cloning vector, pMB1 ori, Ap^(r) Labstock pYA3700 Vector encoding the tightly regulated TT araC P_(araBAD)cassette (65, 66) pYA4181 Suicide vector to generate the ΔP_(fur)::TTaraC P_(araBAD) fur mutation (36) pYA4278 Suicide vector, sacB mobRP4oriR6K; Cm^(r) (67) pYA4895 Suicide vector to generate the ΔaroDmutation pYA4278 pYA5066 Suicide vector to generate the Δ(adiA-adiC)mutation pYA4278 pYA5072 Suicide vector to generate theΔ(P_(adiY)-adiY-P_(adiC)) adiC mutation pYA4278 pYA5075 Intermediatevector for the creation of ΔP_(adiA)::TT araC P_(araBAD) adiA pYA3700pYA5081 Suicide vector specifying the tightly regulated rhaSR P_(rhaBAD)(68) cassette pYA5085 Protein synthesis vector with N-terminal His-tagon AdiA pET28a pYA5089 Suicide vector to generate the ΔP_(adiA)::TT araCP_(araBAD) adiA mutation pYA4278, pYA5075 pYA5093 Suicide vector togenerate the ΔP_(adiA)::TT rhaSR P_(rhabad) adiA pYA5089, mutationpYA5081 pYA5116 Suicide vector to generate ΔendA pYA5103 pYA5119 Suicidevector to generate ΔendA::clcA pYA5116 pYA5120 Suicide vector togenerate ΔcysG::TT araC P_(BAD) gadBC pYA5115 ^(a)In genotypedescriptions, the subscripted number refers to a composite deletion andinsertion of the indicated gene. P, promoter; TT, T4 ip IIItranscription terminator; Cm^(r), chloramphenicol resistance; Kan^(r),kanamycin resistance.

TABLE 2 PCR primers used in the study Name Sequence (5′-3′)Relevant mutation Adi-1 CCGGTACCGATGGGAATATTCCAGCG Δ(adiA-adiC) Adi-2CCGGATCCCTTTTACCCGGTTGTG Δ(adiA-adiC) Adi-3CCGGATCCCCACGTGTAGTTAATGTTATCGC Δ(adiA-adiC) Adi-4CCAAGCTTGGCAATCACGGCTGCC Δ(adiA-adiC) Adi-5 CATGGCATGCCGAATGAGCAAATTCΔ_(PadiA)::TT araC P_(araBAD) adiA Adi-6 CCGGAGATCTTGATAGTGGTATCCGGCTTΔ_(PadiA)::TT araC P_(araBAD) adiA Adi-7CATGGGTACCAGGAGGTAAAAGATGATGAAAG Δ_(PadiA)::TT araC P_(araBAD) adiAAdi-8 CATGGAGCTCCGCCATAATAATCGTG Δ_(PadiA)::TT araC P_(araBAD) adiAAdi-9 CATAGCCGTACCATGCTTCGTCG Regulated adiA constructs Adi-10GCGCTCTAGACGCACCACCGACTTCCAG Δ(P_(adiy)-adiY-P_(adiC)) adiC Adi-11GTATCATACCCCCTCAGAATGTTGCAGCAATACTCAG Δ(P_(adiy)-adiY-P_(adiC)) adiCAdi-12 TTCCCTGAGTATTGCTGCAACATTCTGAGGGGGTATΔ(P_(adiy)-adiY-P_(adiC)) adiC G Adi-13 GCATGGATCCCCAGAACCAGCCGAAGΔ(P_(adiy)-adiY-P_(adiC)) adiC Adi-14 CCGGTACCCGAACTCCGTTATTCCTTACΔ(P_(adiy)-adiY-P_(adiC)) adiC Adi-15 CCAAGCTTCAGATAGCCGACGCCΔ(P_(adiy)-adiY-P_(adiC)) adiC Ara-1 GATTAGCGGATCCTACCTGACGCaraC P_(araBAD) Aro-1 CCCGGGTGCTGGCTGAACAGTTCCTCGAG ΔaroD Aro-2CCGGATCCTCCGGCATTATGCAGGCGTCG ΔaroD Aro-3CCGGATCCGCGTGTCCTGTCAGTTTTTTTTCTTCTC ΔaroD Aro-4TCTAGATCTCCGCATGGGTACATGAAGTTCCGG ΔaroD Fur-1ACATGCATGCTGTGACTGGGATGACTTCTTCCCG ΔPf_(ur)::TT araC P_(BAD) fur Fur-2TCCCCCGGGCACTTTTCCGCAATCAAGGCAG ΔP_(fur)::TT araC P_(BAD) fur Rha-1GCACTCTAGATTAATCTTTCTGCGAATTG ΔP_(adiA)::TT rhaSR P_(rhaBAD)adiA Rha-2GCATCTCGAGGCTGAATTTCATTAC ΔP_(adiA)::TT rhaSR P_(rhaBAD)adiA Rha-3TCAGTAACGAGAAGGTCGCG rhaSR P_(rhaBAD) SQ-1 GCTGAAATATGACTCCACTCAC gapASQ-2 CGTCAACACCAACTTCGTC gapA SQ-3 ACCGACTTCCAGATTATGTTCC adiA SQ-4CGTGTTGATCAGCGTTCCC adiA Gad-1 GGCCGAGCTCCTATCCTGCCGCAAACCΔcysG::TT araC P_(BAD) gadBC Gad-2 CAATTCTAGGATAGAATAATAAAGCGGCCGCGACATTΔcysG::TT araC P_(BAD) gadBC ACCCCTTAATGGTTG Gad-3GTTTTTTTGGGCTAGCCTCGAGAGGAGTTTAAAATGG ΔcysG::TT araC P_(BAD) gadBCATAAGAAG Gad-4 GAATAACAGGGCTTTATTTTAAGATCTAAAAAGGGAGΔcysG::TT araC P_(BAD) gadBC CGATGAAT Gad-5CATCGCTCCCTTTTTAGATCTGCCCTGTTATTCAGGG ΔcysG::TT araC P_(BAD) gadBC CTTTAGad-6 GCATGGTACCCGACCAATGCGGCAAC ΔcysG::TT araC P_(BAD) gadBC Gad-7CCCCCTCGAGGGTATGTTTAAAGCTGTTC ΔcysG::TT araC P_(BAD) gadBC Gad-8GGCACCGTTCGTCGCCCCGGATATCG gadBC seq Gad-9 CAGGTAAAGCTAAGCAGCTCACATTACgadBC seq Gad-10 CGTTCTGATGTCCCATGTGGCACCGG gadBC seq Ara-1CATTAAGGGGTAATGTCGCGGCCGCTTTATTATTCTA ΔcysG::TT araC P_(BAD) gadBCTCCTAGAATTGTG Ara-2 CTTCTTATCCATTTTAAACTCCTCTCGAGGCTAGCCCΔcysG::TT araC P_(BAD) gadBC AAAAAAACG Ara-3 GATTAGCGGATCCTACCTGACGCΔcysG::TT araC P_(BAD) gadBC

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56. Foster, J. W. 1999. When protons attack: microbial strategies ofacid adaptation. Curr Opin Microbiol 2:170-4.

57. de Jonge, R., W. S. Ritmeester, and F. M. van Leusden. 2003.Adaptive responses of Salmonella enterica serovar Typhimurium DT104 andother S. Typhimurium strains and Escherichia coli O157 to low pHenvironments. J Appl Microbiol 94:625-32.

58. Foster, J. W., and H. K. Hall. 1990. Adaptive acidificationtolerance response of Salmonella typhimurium. J Bacteriol 172:771-8.

59. McHan, F., and E. B. Shotts. 1993. Effect of short-chain fatty acidson the growth of Salmonella typhimurium in an in vitro system. Avian Dis37:396-8.

60. Troxell, B., R. C. Fink, S. Porwollik, M. McClelland, and H. M.Hassan. 2011. The Fur regulon in anaerobically grown Salmonella entericasv. Typhimurium: identification of new Fur targets. BMC Microbiol11:236.

61. Roland, K., R. Curtiss, 3rd, and D. Sizemore. 1999. Construction andevaluation of a □cya □crp Salmonella typhimurium strain expressing avianpathogenic Escherichia coli O78 LPS as a vaccine to preventairsacculitis in chickens. Avian Dis 43:429-41.

62. Felix, A., and R. M. Pitt. 1951. The pathogenic and immunogenicactivities of Salmonella typhi in relation to its antigenicconstituents. J Hyg (Lond) 49:92-110.

63. Brenneman, K. E., C. McDonald, S. M. Kelly-Aehle, K. L. Roland, andR. Curtiss, 3rd. 2012. Use of RapidChek® SELECT Salmonella to detectshedding of live attenuated Salmonella enterica serovar Typhi vaccinestrains. J Microbiol Methods 89:137-47.

64. Formal, S. B., G. J. Dammin, E. H. Labrec, and H. Schneider. 1958.Experimental Shigella infections: characteristics of a fatal infectionproduced in guinea pigs. J Bacteriol 75:604-10.

65. Wang, S., Y. Li, H. Shi, G. Scarpellini, A. Torres-Escobar, K. L.Roland, and R. Curtiss, 3rd. 2010. Immune responses to recombinantpneumococcal PsaA antigen delivered by a live attenuated Salmonellavaccine. Infect Immun 78:3258-71.

66. Santander, J., S. Y. Wanda, C. A. Nickerson, and R. Curtiss, 3rd.2007. Role of RpoS in fine-tuning the synthesis of Vi capsularpolysaccharide in Salmonella enterica serotype Typhi. Infect Immun75:1382-92.

67. Kong, Q., J. Yang, Q. Liu, P. Alamuri, K. L. Roland, and R. Curtiss,3rd. 2011. Effect of deletion of genes involved in lipopolysaccharidecore and O-antigen synthesis on virulence and immunogenicity ofSalmonella enterica serovar Typhimurium. Infect Immun 79:4227-39.

68. Kong, W., M. Brovold, J. Tully, L. Benson and R. Curtiss III. 2012.Presented at the ASM 112th General Meeting, San Francisco, Calif., June16-19, 2012.

69. Frey, S. E., H. Hill, K. R. Lottenbach, K. E. Brenneman, Y. Zhang,S. M. Kelly-Aehle, C. McDonald, A. Jansen and Roy Curtiss III. 2013. Aphase I, dose-escalation trial in adults of three recombinant attenuatedSalmonella Typhi vaccine vectors producing Streptococcus pneumoniaesurface protein antigen PspA. Vaccine 31:4874-4880.

Example 6 Sugar-Inducible Amino Acid Decarboxylase Systems

Glutamate Decarboxylase.

The glutamate decarboxylase (GAD) system of E. coli O157:H7 is composedof two homologous decarboxylases (GadA and GadB) and aglutamate/γ-aminobutyric acid antiporter (GadC) (15). GadA and GadB arebiochemically indistinguishable and only one is required for survival atpH 2.5 in E. coli. However, both are required for survival at pH 2 (5,6). In E. coli, this system maintains an internal pH between 4-5 (14).Based on our findings that the antiporter is required for acidresistance in the AdiA system, we took advantage of the fact that gadBand gadC are co-transcribed from a single operon (5) (gadA is located ata distant site on the chromosome (15)) by cloning the gadBC operon andplacing it under transcriptional control of the araC P_(BAD) promoter.To accomplish this, we engineered an operon substitution mutation intothe cysG locus: ΔcysG::TT araC P_(BAD) gadBC. We fused thearabinose-regulator cassette containing araC, the araC promoter, and theP_(BAD) promoter to the flanking region upstream of the cysG locus inSalmonella Typhi Ty2 (FIG. 9). The upstream flanking region wasamplified by PCR from Ty2 using primers Gad-1 and -2 (Table 2); the araCcassette was amplified by PCR from plasmid pYA3700 using primers Ara-1and -2. The two DNA segments were joined by overlap PCR and re-amplifiedwith primers Gad-1 and Ara-2. The overlap PCR product was ligated intopUC18 at the Sal I/XhoI and SacI sites to produce the intermediatevector pYA5105. The strong transcription terminator T4 ip III placedbetween the upstream nirC gene and araC prevents expression of antisenseRNA as well as transcription due to the cysG promoter that remainswithin the coding sequence of nirC.

We fused the gadBC operon with the cysG downstream flanking region.Flanking DNA was amplified by PCR from Ty2 using primers Gad-3 and -4;the gadBC operon was amplified from enterohemorrhagic E. coli strainχ7573 using primers Gad-5 and -6. The two DNA segments were joined byoverlap PCR and re-amplified with primers Gad-3 and -6. The overlapproduct was ligated into pCR2.1 TOPO to generate pYA5101. The upstreamflanking region-araC fusion from pYA5105 and the gadBC operon-downstreamflanking region fusion from pYA5101 were amplified using Gad-1/Ara-2 andGad-3/ -6 respectively (see above) and joined by overlap PCR andre-amplified with primers Gad-1 and -6. This PCR product was ligatedinto pJET1.2 to produce intermediate vector, pYA5115. The intergenicregion between the araC cassette and gadBC operon was confirmed by PCRprimers, Ara-3 and Gad-7. We confirmed the sequence integrity of thegadBC operon using primers Gad-8, -9 and -10. The fusion product frompYA5115 was amplified with primers Gad-1 and -6 and ligated into pYA4278at the AhdI sites, generating the suicide vector pYA5120. pYA5120 wasintroduced into Salmonella Typhi Ty2 phoPQ mutant, χ8444, by conjugationto produce χ11760. The generation and activity of E. coli decarboxylasewithin Salmonella was verified by Western blot, acid resistance survivaland glutamate decarboxylase assay.

Using pYA5120, the araC P_(BAD) gadBC construct (FIG. 9) was introducedinto several S. Typhi strains, each carrying a mutation known toattenuate Salmonella, ΔguaBA (19), ΔphoPQ (9, 10) or Δfur (4, 20). Notethat Salmonella strains with mutations in either phoPQ (8) or fur (7)are extremely acid sensitive. In addition, preliminary results indicatethat our ΔguaBA S. Typhi mutant is also more sensitive to acid shockthan its Ty2 parent (data not shown). Although this phenotype has notbeen documented in the literature, it is interesting to note that aprevious study reported that in E. coli, GuaB synthesis is induced byexposure to low pH (21). The araC P_(BAD) gadBC system conferssugar-inducible acid resistance to all three mutant strains when S.Typhi cells are grown aerobically at pH 7.0 (FIG. 10). In fact, thesurvival of strains carrying this system was greater than wild-type Ty2grown under the same conditions.

Low gastric pH mouse model. While In vitro acid resistance assaysprovide good preliminary information, an animal model will give us abetter idea of how our strains will behave in the clinic. As mentionedabove, the gastric environment of a fasted mouse is around pH 4 (12)compared to a fasted human, whose stomach pH is around 2 (17). Thisdifference can have a profound effect on Salmonella survival and couldprovide data that does not reflect what will happen in humans. To createa gastric pH closer to the human stomach, we took advantage of theobservation that injecting mice with histamine transiently increases HClsecretion by parietal cells lining the stomach (3). Note that in thismodel, mice are injected with the H1 antagonist chlorpheniramine priorto injection with histamine to block an allergic reaction (3). Thisapproach was also used in a study to establish the significance of lowgastric pH as a barrier to infection (16). Based on these observations,we have adapted this model to evaluate the ability of attenuatedSalmonella to transit the stomach (22). In preliminary studies, wemonitored gastric pH in live mice as a function of time after histamineinjection (FIG. 11). Our results indicated that the minimum pH wasreached after one hour.

To validate the low gastric pH mouse model, we monitored survival of avariety of enteric pathogens in fasted mice with or without histamineinjection. For these experiments, cells were grown in LB and eitherchallenged at pH 3.0 in vitro (FIG. 12A) or used to inoculate fastedmice with or without histamine injection. In all cases, survival wasless in the low pH mouse than in the fasted mouse (FIG. 12B). Notsurprisingly, the Vibrio cholerae strain underwent the most killing,consistent with our in vitro results.

Survival of S. Typhi strains carrying sugar-inducible acid resistancesystems in the low gastric pH mouse model. To evaluate the impact ofthese systems in low gastric pH mice, we set up a co-infectionexperiment in which strains with or without the rhamnose inducible adiACgenes carried plasmids with different antibiotic resistance markers.Strains were grown aerobically with 0.1% rhamnose and used to co-infectfasted, low gastric pH mice. Overall, induction of adiAC enhanced thesurvival of all strains (FIG. 13). The greatest increase in survival,10-fold, was observed in the ΔphoPQ strain, consistent with ourpublished in vitro results, which showed that the rhamnose-inducibleadiAC system had the greatest impact on the ΔphoPQ mutant. A similarexperiment was performed to evaluate strains carryingarabinose-inducible gadBC. Survival of all strains was enhanced about10-fold (FIG. 14). Taken together, these results demonstrate that bothsystems are capable of increasing the survival of a variety of S. Typhistrains carrying mutations that can be used to attenuate virulence foruse as human vaccines.

Lysine decarboxylase system. In addition to the adiAC and gadBC systems,resistance to acid shock can also be mediated by the AR4 system, lysinedecarboxylase and lysine:cadaverine antiporter, encoded by cadA andcadB, respectively (13). In Salmonella, the cadAB genes are present asan operon and are induced by low pH and anaerobiosis, in aCadC-dependent manner when lysine is present (13). The cadAB system alsoplays a role in the acid tolerance response (13). This system greatlyenhances the ability of Salmonella to survive an acid challenge at pH2.3 after overnight anaerobic growth in a rich medium at pH 5 (18).Unlike adiAC or gadBC, this system can also enhance the growth ofSalmonella at a moderately acidic pH of 4.5. Notably, this is observedunder both aerobic and anaerobic growth conditions, which may be ofadditional benefit during vaccine preparation and transit through thestomach. In addition, this system lead to an increase the pH external tothe cell, which may have benefits in the macrophage lysosome. Toevaluate this system, we will construct S. Typhi vaccine strains (e.gΔphoP, Δfur, ΔguaAB) in which cadAB expression is driven by asugar-inducible promoter and characterize them in vitro, as we have donefor adiAC and gadBC.

Construction of an S. Typhi vaccine strain with enhanced survival at pH2.0. (i) Addition of gadA to strains carrying a sugar-regulated gadBCoperon. In E. coli, GadA and GadB are nearly identical isoforms ofglutamate decarboxylase located at different places on the chromosome(15). The gadBC operon alone is effective acid protection at pH 2.5,while both gadA and gadBC are required for maximum rates of survival atpH 2.0 (2). We observed similar results in that insertion of the gadBCinto S. Typhi protects well against acid shock down to pH 2.5 (FIG. 10),but is ineffective against a pH 2.0 challenge (data not shown). Thus, itmay be possible to enhance S. Typhi survival by introduction of an araCP_(BAD) gadA construct into strains already carrying araC P_(BAD) gadBC.The gadA gene will be inserted into the chromosome by substituting itfor araE. Deletion of araE does not affect the virulence of S.Typhimurium (data not shown). The construction of the araC P_(BAD) gadAcassette will be done essentially as we have described for araC P_(BAD)adiA (1) and araC P_(BAD) gadBC.

Addition of chloride channel protein ClcA from E. coli. Survival belowpH 3 in E. coli is predicated on the reversal of the transmembranepotential (14). Currently no data are available to indicate whether thisoccurs in Salmonella, but it is likely that this will be the case. Totest this, we will introduce the ClC chloride channel (eriC/clcA) fromE. coli, using suicide plasmid pYA5119, as this has been shown to be anessential player in acid resistance by preventing membranehyperpolarization at low pH (11, 14). Although S. Typhimurium and S.Typhi contain genes designated as ClC channels, alignment with the E.coli eriC reveals no significant homology and casts doubt on the abilityof the Salmonella channels to serve as a substitute at low pH.

References Cited in Example 6

1. Brenneman, K. E., C. Willingham, W. Kong, R. Curtiss, 3rd, and K. L.Roland. 2013. Low pH Rescue of Acid-Sensitive Salmonella Typhi Strainsby a Rhamnose-Regulated Arginine Decarboxylase System. J Bacteriol.195:3062-3072.

2. Castanie-Cornet, M. P., T. A. Penfound, D. Smith, J. F. Elliott, andJ. W. Foster. 1999. Control of acid resistance in Escherichia coli. JBacteriol 181:3525-3535.

3. Chew, C. S., X. Chen, R. J. Bollag, C. Isales, K. H. Ding, and H.Zhang. 2008. Targeted disruption of the Lasp-1 gene is linked toincreases in histamine-stimulated gastric HCl secretion. Am J PhysiolGastrointest Liver Physiol 295:G37-G44.

4. Curtiss, R., 3rd, S. Y. Wanda, B. M. Gunn, X. Zhang, S. A. Tinge, V.Ananthnarayan, H. Mo, S. Wang, and W. Kong. 2009. Salmonella strainswith regulated delayed attenuation in vivo. Infect Immun.

5. De Biase, D., A. Tramonti, F. Bossa, and P. Visca. 1999. The responseto stationary-phase stress conditions in Escherichia coli: role andregulation of the glutamic acid decarboxylase system. Mol Microbiol32:1198-1211.

6. De Biase, D., A. Tramonti, R. A. John, and F. Bossa. 1996. Isolation,overexpression, and biochemical characterization of the two isoforms ofglutamic acid decarboxylase from Escherichia coli. Protein Expr Purif8:430-438.

7. Foster, J. W. 1991. Salmonella acid shock proteins are required forthe adaptive acid tolerance response. J Bacteriol 173:6896-6902.

8. Foster, J. W., and H. K. Hall. 1990. Adaptive acidification toleranceresponse of Salmonella typhimurium. J Bacteriol 172:771-778.

9. Galan, J. E., and R. Curtiss, 3rd. 1989. Virulence and vaccinepotential of phoP mutants of Salmonella Typhimurium. Microb Pathog6:433-443.

10. Hohmann, E. L., C. A. Oletta, K. P. Killeen, and S. I. Miller. 1996.phoP/phoQ-deleted Salmonella typhi (Ty800) is a safe and immunogenicsingle-dose typhoid fever vaccine in volunteers. J Infect Dis173:1408-1414.

11. Iyer, R., T. M. Iverson, A. Accardi, and C. Miller. 2002. Abiological role for prokaryotic ClC chloride channels. Nature419:715-718.

12. McConnell, E. L., A. W. Basit, and S. Murdan. 2008. Measurements ofrat and mouse gastrointestinal pH, fluid and lymphoid tissue, andimplications for in-vivo experiments. J Pharm Pharmacol 60:63-70.

13. Neely, M. N., and E. R. Olson. 1996. Kinetics of expression of theEscherichia coli cad operon as a function of pH and lysine. J Bacteriol178:5522-5528.

14. Richard, H., and J. W. Foster. 2004. Escherichia coli glutamate- andarginine-dependent acid resistance systems increase internal pH andreverse transmembrane potential. J Bacteriol 186:6032-6041.

15. Smith, D. K., T. Kassam, B. Singh, and J. F. Elliott. 1992.Escherichia coli has two homologous glutamate decarboxylase genes thatmap to distinct loci. J Bacteriol 174:5820-5826.

16. Tennant, S. M., E. L. Hartland, T. Phumoonna, D. Lyras, J. I. Rood,R. M. Robins-Browne, and I. R. van Driel. 2008. Influence of gastricacid on susceptibility to infection with ingested bacterial pathogens.Infect Immun 76:639-645.

17. Verdu, E. F., R. Fraser, D. Armstrong, and A. L. Blum. 1994. Effectsof omeprazole and lansoprazole on 24-hour intragastric pH inHelicobacter pylori-positive volunteers. Scand J Gastroenterol29:1065-1069.

18. Viala, J. P., S. Meresse, B. Pocachard, A. A. Guilhon, L. Aussel,and F. Barras. 2011. Sensing and adaptation to low pH mediated byinducible amino acid decarboxylases in Salmonella. PLoS One 6:e22397.

19. Wang, J. Y., M. F. Pasetti, F. R. Noriega, R. J. Anderson, S. S.Wasserman, J. E. Galen, M. B. Sztein, and M. M. Levine. 2001.Construction, genotypic and phenotypic characterization, andimmunogenicity of attenuated ΔguaBA Salmonella enterica serovar Typhistrain CVD 915. Infect Immun 69:4734-4741.

20. Wilmes-Riesenberg, M. R., B. Bearson, J. W. Foster, and R. Curtiss,3rd. 1996. Role of the acid tolerance response in virulence ofSalmonella typhimurium. Infect Immun 64:1085-1092.

21. Yohannes, E., D. M. Barnhart, and J. L. Slonczewski. 2004.pH-dependent catabolic protein expression during anaerobic growth ofEscherichia coli K-12. J Bacteriol 186:192-199.

22. Brenneman, K. E., C. Willingham, J. Kilbourne, R. Curtiss III andK.L. Roland. 2014. A low gastric pH mouse model to evaluate liveattenuated bacterial vaccines. PLoS One 9:e87411.

Example 7 Urease System

Another method to increase the acid resistance of Salmonella vaccinestrains is to introduce the Ni-dependent urease system of Helicobacterpylori. The urease system is a unique acid resistance strategy,different from the others described herein. Helicobacter survives atextremely low pH not by acid resistance (temporary halt of all metabolicactivities while protons are consumed and exported away from the cell),but by acid acclimation, where the cytoplasm is buffered to almostneutral pH (pH 5-7) and metabolic processes can still occur [1]. Thissystem is more complex than the GAD or ADI systems and involves manymore gene products. Urea from the gastric fluid is allowed to enter thecell at low pH by UreI (a proton-gated urea channel) [2]. The urea isthen converted to ammonia by the urease (composed of UreA and UreB) [3].The ammonia freely diffuses into the periplasm, where it is used inconjunction with H₂CO₃ generated by carbonic anhydrase (named HP1186) toestablish a periplasmic reservoir of bicarbonate buffer [4]. This systemconsumes two protons per reaction cycle, as opposed to one proton percycle in the GAD and ADI systems. The urease system has the additionaladvantage of consuming protons in the periplasm (as opposed to thecytoplasm), which further protects essential cytoplasmic molecules.

The urease system involves more genes than the decarboxylase systems,and for this system, it is unlikely that all of these genes must beunder the control of a regulatable promoter, only the ones that directlycontribute to proton consumption (ureAB and HP1186). These genes will beintroduced into the Salmonella chromosome under the control of asugar-regulatable promoter such as rhaRS-P_(rhaBAD)

The additional components of this system, ureI—encoding the proton-gatedurea channel—and ureEFGH—encoding a chaperone complex necessary toincorporate Ni ions into the urease apoenzyme [5]—will be introducedinto the chromosome under the control of a constitutive promoter such asP_(Ipp).

References Cited in Example 7

1. Sachs, G., et al., The gastric biology of Helicobacter pylori. AnnuRev

Physiol, 2003. 65: p. 349-69.

2. Rektorschek, M., et al., Acid resistance of Helicobacter pyloridepends on the UreI membrane protein and an inner membrane protonbarrier. Mol Microbiol, 2000. 36(1): p. 141-52.

3. Labigne, A., V. Cussac, and P. Courcoux, Shuttle cloning andnucleotide sequences of Helicobacter pylori genes responsible for ureaseactivity. J Bacteriol, 1991. 173(6): p. 1920-31.

4. Marcus, E. A., et al., The periplasmic alpha-carbonic anhydraseactivity of Helicobacter pylori is essential for acid acclimation. JBacteriol, 2005. 187(2): p. 729-38.

5. Park, J. U., et al., Effect of the urease accessory genes onactivation of the Helicobacter pylori urease apoprotein. Mol Cells,2005. 20(3): p. 371-7.

Example 8 The Presence of Acid Resistance Systems Increases theImmunogenicity of a Live Attenuated Salmonella Vaccine

To investigate the effect of our system on immunogenicity, weconstructed derivatives of S. Typhimurium ΔphoPQ strain χ8089 thatcarried either the ΔP_(adiA)::TT araC P_(BAD) adiAC or the ΔcysG::TTaraC P_(BAD) gadBC systems in which adiAC or gadBC expression isregulated by arabinose. Strains were grown in the presence of 0.1%arabinose and used to inoculate mice treated with histamine to induce alow gastric pH. Mice were given various doses of each strain, 1×10⁴,1×10⁶ or 1×10⁸ CFU. Mice were inoculated with the same dose of the samestrains on days 0 and 28 (low gastric pH induced prior to both doses).Mice were challenged on day 49 with 1×10⁸ CFU of wild-type S.Typhimurium strain χ3761 and observed for two weeks post challenge. Theresults (Table 3) indicated that only strains carrying thearabinose-inducible acid resistance system were protective whenadministered at doses of 1×10⁶ CFU or 1×10⁸ CFU. None were protective atthe 1×10⁴ dose. These results indicate that an acid-resistance systemcan enhance the immunogenicity of live attenuated Salmonella vaccines.

TABLE 3 Effect of arabinose-inducible acid resistance systems onprotective efficacy of S. Typhimurium ΔphoPQ strains Immunizing DosePost challenge Strain* (CFU) live/total χ8089 1 × 10⁴ 0/5 χ11808 1 × 10⁴0/5 χ11789 1 × 10⁴ 1/5 χ8089 1 × 10⁶ 0/5 χ11808 1 × 10⁶ 3/5 χ11789 1 ×10⁶ 2/5 χ8089 1 × 10⁸ 0/5 χ11808 1 × 10⁸ 5/5 χ11789 1 × 10⁸ 5/5 PBS —0/5 *genotypes - χ8089 = ΔphoPQ χ11808 = ΔphoPQ ΔP_(adiA)::TT araCP_(BAD) adiAC χ11789 = ΔphoPQ ΔcysG::TT araC P_(BAD) gadBCMice were immunized day 0 and 28 (acid mice both times). Challenge onday 49 with 1×10⁸ CFU wild-type S. Typhimurium χ3761. Mice observed for21 days post challenge

Example 9 Use of Acid-Resistance Systems in Probiotic Bacteria

Probiotics are live microorganisms, which may provide beneficial effectswhen ingested. Although the mechanisms underlying still remain poorlyunderstood, studies have demonstrated that the probiotics canefficiently inhibit the impact of pathogens in the gut either bydirectly by growth competition or indirectly via production ofinhibitory substances such as bacteriocins [1]. Typical probiotics suchas Lactic acid bacteria, bifidobacteria, certain yeasts and bacilli havebeen well studied for decades and show beneficial effects on treatmentof antibiotic-associated diarrhea [2], lactose intolerance [3] and coloncancer [4]. The ability of probiotics to improve host immune function[5,6], modulate inflammatory and hypersensitivity responses [5] havealso been documented. The Escherichia coli Nissle 1917 strain has beenused as a probiotic agent in human and animal medicine to treat chronicinflammatory and infectious diseases of the human and animal intestine[7].

Similar to live bacterial vaccines, probiotic strains are administeredorally a must survive the low pH stomach environment in order to beeffective. The regulatable acid resistance systems may serve to increasethe survival of probiotic bacteria during passage through the stomach.

References cited in Example 9

1. Sanders M E. Impact of probiotics on colonizing microbiota of thegut. J Clin Gastroenterol 45 Suppl, S115-119 (2011).

2. D'Souza A L, Rajkumar C, Cooke J, Bulpitt C J. Probiotics inprevention of antibiotic associated diarrhoea: meta-analysis.Bmj324(7350), 1361 (2002).

3. Sanders M E. Considerations for use of probiotic bacteria to modulatehuman health. The Journal of nutrition 130(2S Suppl), 384S-390S (2000).

4. Brady L J, Gallaher D D, Busta F F. The role of probiotic cultures inthe prevention of colon cancer. The Journal of nutrition 130(2S Suppl),410S-414S (2000).

5. Reid G, Jass J, Sebulsky M T, McCormick J K. Potential uses ofprobiotics in clinical practice. Clinical microbiology reviews 16(4),658-672 (2003).

6. Ouwehand A C, Salminen S, Isolauri E. Probiotics: an overview ofbeneficial effects. Antonie van Leeuwenhoek 82(1-4), 279-289 (2002).

7. Kamada N, Inoue N, Hisamatsu T et aL Nonpathogenic Escherichia colistrain Nissle1917 prevents murine acute and chronic colitis.Inflammatory bowel diseases 11(5), 455-463 (2005).

Example 10 Use of Acid Resistance Systems in a Live AttenuatedSalmonella enterica Serovar Gallinarum Vaccine for Poultry

Salmonella enterica serovar Gallinarum (S. Gallinarum) is a host-adaptedpathogen that causes fowl typhoid—an important disease of poultry (1).Fowl typhoid is a septicemic disease with a typically short course andsignificant morbidity and mortality, which can reach as high as 100%(2). The disease occurs primarily in mature flocks, although birds ofall ages may be infected. Certain mutations of S. Gallinarum, such asΔfur mutant χ11797 and Δfur Apmi mutant χ11798, are effective whendelivered intramuscularly, but are only partially effective whendelivered orally. This discrepancy can be explained by the acidsensitivity of these strains (FIG. 15).

Thus, it may be that because the double mutant is more sensitive to lowpH than the Δfur strain (FIG. 15), it does not survive as well duringpassage through the low pH environment of the proventriculus. If this isthe case, pH sensitivity may also help to explain our conflictingresults with fur mutant χ11797, which was protective when orallyadministered to chicks (Table 4), but was less effective when orallyadministered to older layers. The proventricular pH in chickens changesduring the first few weeks of life, ranging from a pH of about 5 at twodays of age to about 3 to 3.5 by fifteen days of age (3). Thus, it ispossible that survival of strain χ11797 was greater in chicks than inthe older birds used in our study. When we bypassed the gastriccompartment by intramuscular injection, the χ11797 was able to elicit aprotective response (Table 4). The increased acid sensitivity of χ11798could account for its lack of immunogenicity in chicks.

Introduction of an inducible acid resistance system can overcome thisacid sensitivity. We introduced the arabinose-regulated gadBC system byintroducing suicide plasmid pYA5120 (Table 1) into strains χ11797 andχ11798 by conjugation. Transconjugants are selected on LB plates with 20μg/ml chloramphenicol. Loss of the integrated suicide plasmid isselected for on LB plates with 5% sucrose. The resulting strains derivedfrom χ11797 and χ11798 are designated χ12040 and χ12041, respectively.When the strains are grown in the presence of 0.05% arabinose, thepresence of the gadBC system increased the acid resistance of bothstrains to wild-type levels (FIG. 16). Thus, inclusion of the gadBCsystem can enhance acid resistance of S. Gallinarum vaccine strains.

TABLE 4 Efficacy of Δfur and Δfur Δpmi mutants as vaccines against S.Gallinarum challenge in chickens. Age of S. Gallinarum bird at Route of% vaccine vacci- vacci- sur- strain Genotype nation Breed nation vivalχ11797 Δfur 5 days   Rhode oral 91% Island Red χ11798 Δpmi 5 days  Rhode oral 22% Δfur Island Red Buffer — 5 days   Rhode oral 18% IslandRed χ11797 Δfur 7 weeks Brown oral 50% layers χ11797 Δfur 7 weeks Brownintra- 100%  layers muscular χ11798 Δpmi 7 weeks Brown intra- 100%  Δfurlayers muscular No 38% vaccine

References Cited in Example 10

1. Shivaprasad H L. 2000. Fowl typhoid and pullorum disease. Rev SciTech 19:405-424.

2. Barrow P A, Freitas Neto O C. 2011. Pullorum disease and fowltyphoid—new thoughts on old diseases: a review. Avian Pathol 40:1-13.

3. Rynsburger J M, Classen H L. 2007. Effect of age on intestinal pH ofbroiler chickens, International Poultry Scientific Forum, Atlanta, Ga.,USA.

Example 11 Use of Acid Resistance Systems in Salmonella enterica SerovarDublin Vaccines

Salmonella Dublin is host-adapted for cattle, causing systemicinfections, enteritis and abortions (1). It can also cause human disease(1). As in non-ruminants, the gastrointestinal tract of cattle iscomposed of low pH compartments in which acid-sensitive bacteria arekilled (2). During transit through the ruminant gastrointestinal tract,Salmonella encounters various acidic conditions. Volatile fatty acid(VFA) concentrations are high in the rumen of grain-fed animals, and thepH may vary from 5.0 to 6.5. In these conditions, VFAs are in theundissociated form and can freely enter the bacterial cells, dissociate,and acidify the cytosol. In hay-fed animals, less fermentation occurs inthe rumen, and the pH remains between 6.5 and 7. In the abomasum,Salmonella can encounter strongly acidic conditions, regardless of thediet, due to the presence of mineral acids, resulting in a pH below 3.Then the pH increases from the proximal part to the distal part of thesmall intestine, cecum and colon. Inclusion of an inducible acidresistance system into live attenuated S. Dublin vaccines will enhancesurvival during low pH encounters in orally vaccinated cattle, leadingto improved immunogenicity and efficacy. Introduction of an inducibleacid resistance system can be accomplished by step-wise introduction ofthe ΔP_(adiA):TT AP rhaSR P_(rhaBAD) adiA using plasmid pYA5093 followedby introduction of the Δ(P_(adiY)-adiY-P_(adiC)) adiC mutation usingsuicide plasmid pYA5072 to yield the rhamnose-regulated adiA systemΔP_(adiA)::TT rhaSR P_(rhaBAD) adiA Δ(P_(adiY)-adiY-P_(adiC)) adiC.Alternatively, the arabinose-regulated gadBC system can be introducedusing plasmid pYA5120 (ΔcysG::TT araC P_(BAD) gadBC).

References Cited in Example 11

1. Uzzau S, Brown D J, Wallis T, Rubino S, Leori G, Bernard S, CasadesusJ, Platt D J, Olsen J E. 2000. Host adapted serotypes of Salmonellaenterica. Epidemiol Infect 125:229-255.

2. Chaucheyras-Durand F, Faqir F, Ameilbonne A, Rozand C, Martin C.2010. Fates of acid-resistant and non-acid-resistant Shigatoxin-producing Escherichia coli strains in ruminant digestive contentsin the absence and presence of probiotics. Appl Environ Microbiol76:640-647.

Example 12 Survival of Vaccine Strains in Low Gastric pH Mouse Model isEnhanced By Co-Administration of Ensure® Nutrition Shake

Methods. Strains used in this study are shown in Table 5. Plasmids areshown in Table 6. Six week old, female BALB/c mice (Charles RiverLaboratories, Wilmington, Mass., USA) were fasted without food or waterfor 6 h prior to the start of the experiment. Mice received thehistamine H₁-receptor antagonist chlorpheniramine (0.3 mg/kg)subcutaneously to prevent allergy/anaphylaxis symptoms. Prior toinoculation, low gastric pH was induced by subcutaneous injection ofhistamine dihydrochloride (10 mg/kg). Strains were grown to late logphase (optical density at 600 nm of 0.9), then pelleted and resuspendedin PBS at a concentration of 5×10¹⁰ CFU/ml. Groups of 5 mice were orallyinoculated 50 min after the administration of histamine (1). Low gastricpH was treated with sodium bicarbonate, Ensure, or nothing. Groups thatwere treated with bicarbonate received 40 μl of a 1.3% sodiumbicarbonate solution orally 10 minutes prior to inoculation and anadditional 10 μl 10 minutes after immunization. Groups that were treatedwith Ensure received 20 μl of Ensure® Nutrition shake (milk chocolateflavor) 10 minutes prior to inoculation and an additional 20 μl 10minutes after immunization.

Gastric transit assays. Mice were inoculated as described above. Strainsused in the gastric transit assays contained the low copy number plasmidpWSK129 (Kan^(r)) to allow for precise quantitation of strain numbers inthe non-sterile environment of the gastrointestinal tract. Mice wereeuthanized 1 h after inoculation and the entire small intestine wasremoved, homogenized and serially diluted. Samples were plated onto LBagar containing 0.2% arabinose with kanamycin to determine the number ofviable bacteria present following low pH gastric transit. The survivalof the Ensure® and bicarbonate groups was compared to the control groupusing the Mann-Whitney test. Statistical analysis was performed byGraphPad Prism version 6.00 for Windows (Graph Pad Software, La JollaCalif. USA).

Results. To examine the ability of bicarbonate and Ensure® to combatgastric pH, these were used to buffer the stomach pH of mice. Becausethe gastric pH of a fasted mouse is about pH 4.0 and the gastric pH of afasted human is about pH 1-2 (3,5,7), gastric acid secretion was inducedin mice prior to immunization to better mimic the situation in humans.Using this protocol, the pH in the mouse stomach is reduced to around1.5. Mice received either bicarbonate or Ensure® prior to andimmediately following inoculation. Control mice received no treatment.Vaccine viability was measured following gastric transit (FIG. 17). Fortwo of the three S. Typhi vaccine strains and the S. Typhimurium modelstrain, administration of Ensure® significantly increased the number ofviable cells that reached the small intestine (p=0.0019 forχ9633(pYA4088), p=0.0256 for χ9640(pY4088) and p=0.0006 forχ9558(pYA4088)). This was a 599-, 75.0- and 647-fold increase,respectively, in the geometric mean number of viable cells to reach theileum. Administration of Ensure® prior to and following immunization didnot significantly affect the ability of χ9639(pYA4088) to transit thegastric compartment (p=0.2317), quite possibly due to the mutation inthe rpoS gene which confers acid sensitivity. Bicarbonate similarlyimproved the survival of χ9640(pYA4088) (p=0.0190) and χ9558(pYA4088)(p=0.0379) during gastric transit, resulting in a 41.0- and 8.79-foldincrease in the geometric mean number of cells to reach the ileum,respectively. Administration of bicarbonate did not significantly impactthe survival of χ9633(pYA4088) or χ9639(pYA4088) (p=0.2317 and 0.4945,respectively). Overall, Ensure® worked best to protect these strainsfrom low gastric pH. We infer that inclusion of a sugar-inducible acidresistance system such as araC P_(BAD) gadBC or ΔP_(adiA)::TT rhaSRP_(rhaBAD) adiA Δ(P_(adiY)-adiY-P_(adiC))-adiC, will enhance survival ofthese vaccines further.

TABLE 5 Strains used in gastric transit assays demonstrating protectiveeffect of Ensure ® Nutrition shake. Sal- Ref- monella er- Strain SerovarGenotype/Phenotype^(a) ence χ9558 Typhi- Δpmi Δ(gmd-fcl) ΔP_(fur)::TTaraC P_(BAD) fur (4) murium ΔP_(crp)::TT araC P_(BAD) crp ΔasdA:TT araCP_(BAD) c2 ΔaraE ΔaraBAD ΔrelA::araC P_(BAD) lacI TT ΔsopB ΔagfBAC,RpoS⁺ χ9633 Typhi ΔP_(crp)::TT araC P_(BAD) crp ΔP_(fur)::TT araCP_(BAD) (6) fur Δpmi Δ(gmd-fcl) ΔsopB ΔrelA::araC P_(BAD) lacI TT ΔaraEΔaraBAD ΔtviABCDE ΔagfBAC ΔasdA, RpoS⁺ χ9639 Typhi ΔP_(crp)::TT araCP_(BAD) crp ΔP_(fur)::TT araC P_(BAD) (6) fur Δpmi Δ(gmd-fcl)ΔrelA::araC P_(BAD) lacI TT ΔaraE ΔtviABCDE ΔagfBAC ΔsopB ΔasdA, RpoS⁻χ9640 Typhi ΔP_(crp)::TT araC P_(BAD) crp ΔP_(fur)::TT araC P_(BAD) (6)fur Δpmi Δ(gmd-fcl) ΔrelA::araC P_(BAD) lacI TT ΔaraE ΔtviABCDE ΔagfBACΔsopB ΔasdA RpoS⁺ ^(a)In genotype descriptions, the subscripted numberrefers to a composite deletion and insertion of the indicated gene. P,promoter; TT, T4 ip III transcription terminator.

TABLE 6 Plasmids used in this study Plasmid Description^(a) ReferencepWSK129 pSC101 ori, Kan^(r) (8) pYA3493 pBR ori, Asd⁺ vector with blaSS-based (2) periplasmic antigen secretion pYA4088 Encodes the α-helicalregion of PspA (9) (aa 3-285) in pYA3493 ^(a)ori, replication of origin;SS, secretion signal; Kan^(r), kanamycin resistance

References Cited for Example 12

1. Brenneman, K. E., C. Willingham, J. A. Kilbourne, R. Curtiss, 3rd andK. L. Roland. A low gastric pH mouse model to evaluate live attenuatedbacterial vaccines. PLoS One 9: e87411.2014

2. Kang, H. Y., J. Srinivasan and R. Curtiss, 3rd. Immune responses torecombinant pneumococcal PspA antigen delivered by live attenuatedSalmonella enterica serovar Typhimurium vaccine. Infect Immun 70:1739-1749.2002

3. Kararli, T. T. Comparison of the gastrointestinal anatomy,physiology, and biochemistry of humans and commonly used laboratoryanimals. Biopharm Drug Dispos 16: 351-380.1995

4. Li, Y., S. Wang, G. Scarpellini, B. Gunn, W. Xin, S. Y. Wanda, K. L.Roland and R. Curtiss, 3rd. Evaluation of new generation Salmonellaenterica serovar Typhimurium vaccines with regulated delayed attenuationto induce immune responses against PspA. Proc Natl Acad Sci USA 106:593-598.2009

5. McConnell, E. L., A. W. Basit and S. Murdan. Measurements of rat andmouse gastrointestinal pH, fluid and lymphoid tissue, and implicationsfor in-vivo experiments. J Pharm Pharmacol 60: 63-70.2008

6. Shi, H., J. Santander, K. E. Brenneman, S. Y. Wanda, S. Wang, P.Senechal, W. Sun, K. L. Roland and R. Curtiss. Live recombinantSalmonella Typhi vaccines constructed to investigate the role of rpoS ineliciting immunity to a heterologous antigen. PLoS One 5: e11142.2010

7. Verdu, E., F. Viani, D. Armstrong, R. Fraser, H. H. Siegrist, B.Pignatelli, J. P. Idstrom, C. Cederberg, A. L. Blum and M. Fried. Effectof omeprazole on intragastric bacterial counts, nitrates, nitrites, andN-nitroso compounds. Gut 35: 455-460.1994

8. Wang, R. F. and S. R. Kushner. Construction of versatilelow-copy-number vectors for cloning, sequencing and gene expression inEscherichia coli. Gene 100: 195-199.1991

9. Xin, W., S. Y. Wanda, Y. Li, S. Wang, H. Mo and R. Curtiss, 3rd.Analysis of type II secretion of recombinant pneumococcal PspA and PspCin a Salmonella enterica serovar Typhimurium vaccine with regulateddelayed antigen synthesis. Infect Immun 76: 3241-3254.2008

What is claimed is:
 1. A recombinant attenuated derivative of apathogenic enteric bacterium comprising at least one of the following:a) a regulatable promoter operably linked to a nucleic acid encoding anarginine decarboxylase and a nucleic acid encoding an arginine agmatineantiporter; b) a regulatable promoter operably linked to a nucleic acidencoding a glutamate decarboxylase and a nucleic acid encoding aglutamate/γ-aminobutyric acid antiporter; or c) a regulatable promoteroperably linked to a nucleic acid encoding a lysine decarboxylase and anucleic acid encoding a lysine/cadaverine antiporter.
 2. The recombinantbacterium of claim 1, wherein the enteric bacterium is either naturallyacid sensitive or becomes more acid sensitive because of attenuatingmutations, such that in the absence of induction of the regulatablepromoter, the recombinant bacterium is acid sensitive, but uponinduction of the regulatable promoter, the recombinant bacteriumdisplays an increase in acid resistance.
 3. The recombinant bacterium ofclaim 2, wherein the bacterium is acid sensitive because of a mutationin a nucleic acid sequence selected from the group consisting of rpoS,fur, phoPQ and guaBA.
 4. The recombinant bacterium of claim 1, whereinthe regulatable promoter is induced by a sugar.
 5. The recombinantbacterium of claim 4, wherein the sugar is selected from the groupconsisting of arabinose and rhamnose.
 6. The recombinant bacterium ofclaim 1, wherein the bacterium comprises at least one mutation selectedfrom the group consisting of: a) ΔP_(adiA)::TT araC P_(araBAD) ad/ACmutation; b) ΔP_(adiA)::TT rhaSR P_(rhaBAD) adiAC mutation; c) rhaSRP_(rhaBAD) gadBC mutation; d) araC P_(araBAD) gadBC mutation; e)ΔP_(cadB)::TT rhaSR P_(rhaBAD) cadBA mutation; and f) ΔP_(cadB)::TT araCP_(araBAD) cadBA mutation.
 7. The recombinant bacterium of claim 6,wherein the bacterium further comprises at least one element selectedfrom the group consisting of: a) a regulatable promoter operably linkedto gadA; b) the cicA gene from E. coli transcribed from its own nativepromoter, a heterologous constitutive promoter or a heterologousregulatable promoter; and c) a Ni-dependent urease system from H.pylori.
 8. The recombinant bacterium of claim 1, wherein the bacteriumis a Salmonella bacterium and: a) the nucleic acid encoding the argininedecarboxylase is a Salmonella adiA sequence and the nucleic acidencoding the arginine agmatine antiporter is a Salmonella adiC sequence;or b) the nucleic acid encoding the glutamate decarboxylase is an E.coli gadB and/or an E. coli gadA sequence and the nucleic acid encodingthe glutamate γ-aminobutyric acid antiporter is an E. coli gadCsequence; or c) the nucleic acid encoding the lysine decarboxylase is aSalmonella cadA sequence and the nucleic acid encoding thelysine/cadaverine antiporter is a cadB sequence.
 9. A vaccinecomposition, the composition comprising a bacterium of claim
 1. 10. Amethod for increasing the acid resistance of an acid sensitivebacterium, the method comprising introducing into the acid sensitivebacterium a cassette comprising at least one of the following: a) aregulatable promoter operably linked to a nucleic acid encoding anarginine decarboxylase and a nucleic acid encoding an arginine agmatineantiporter; b) a regulatable promoter operably linked to a nucleic acidencoding a glutamate decarboxylase and a nucleic acid encoding aglutamate/γ-aminobutyric acid antiporter; or c) a regulatable promoteroperably linked to a nucleic acid encoding a lysine decarboxylase and anucleic acid encoding a lysine/cadaverine antiporter, such that in theabsence of induction of the regulatable promoter, the recombinantbacterium is acid sensitive, but upon induction of the regulatablepromoter, the recombinant bacterium displays an increase in acidresistance.
 11. The method of claim 9, wherein the bacterium comprises amutation in at least one nucleic acid sequence selected from the groupconsisting of rpoS, fur, phoPQ and guaBA.
 12. The method of claim 9,wherein the regulatable promoter is induced by a sugar.
 13. The methodof claim 11, wherein the sugar is selected from the group consisting ofarabinose and rhamnose.
 14. The method of claim 9, wherein the bacteriumcomprises at least one mutation selected from the group consisting of:a) ΔP_(adiA)::TT araC P_(araBAD) adiAC mutation; b) AP_(adiA)::TT rhaSRP_(rhaBAD)adiAC mutation; c) rhaSR P_(rhaBAD) gadBC mutation; d) araCP_(araBAD) gadBC mutation; e) AP_(cadB)::TT rhaSR P_(rhaBAD) cadBAmutation; and f) AP_(cadB)::TT araC P_(araBAD) cadBA mutation.
 15. Therecombinant bacterium of claim 14, wherein the bacterium furthercomprises at least one element selected from the group consisting of: a)a regulatable promoter operably linked to gadA; b) the cicA gene from E.coli transcribed from its own native promoter, a heterologousconstitutive promoter or a heterologous regulatable promoter; and c) aNi-dependent urease system from H. pylori.
 16. The method of claim 9,wherein the bacterium is a Salmonella bacterium and: a) the nucleic acidencoding the arginine decarboxylase is a Salmonella adiA sequence andthe nucleic acid encoding the arginine agmatine antiporter is aSalmonella adiC sequence; or b) the nucleic acid encoding the glutamatedecarboxylase is an E. coli gadB and/or an E. coli gadA sequence and thenucleic acid encoding the glutamate γ-aminobutyric acid antiporter is anE. coli gadC sequence; or c) the nucleic acid encoding the lysinedecarboxylase is a Salmonella cadA sequence and the nucleic acidencoding the lysine/cadaverine antiporter is a cadB sequence.
 17. Arecombinant Salmonella bacterium, the bacterium comprising a regulatablepromoter operably linked to at least one nucleic acid selected from thegroup consisting of: a) adiA and adiC; b) gadB and gadC; and c) cadB andcadA.
 18. The recombinant Salmonella bacterium of claim 17, wherein thebacterium further comprises a mutation in at least one nucleic acidsequence selected from the group consisting of rpoS, fur, phoPQ andguaBA that renders the bacterium acid sensitive.
 19. The recombinantSalmonella bacterium of claim 17, wherein the bacterium furthercomprises at least one element selected from the group consisting of: a)a regulatable promoter operably linked to gadA; b) the clcA gene from E.coli transcribed from its own native promoter, a heterologousconstitutive promoter or a heterologous regulatable promoter; and c) aNi-dependent urease system from H. pylori.
 20. A vaccine composition,the composition comprising a bacterium of claim 17.